Starting phenix.real_space_refine on Thu Mar 5 04:42:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ytv_10924/03_2026/6ytv_10924.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ytv_10924/03_2026/6ytv_10924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ytv_10924/03_2026/6ytv_10924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ytv_10924/03_2026/6ytv_10924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ytv_10924/03_2026/6ytv_10924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ytv_10924/03_2026/6ytv_10924.map" } resolution = 4.39 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 12760 2.51 5 N 3250 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19560 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.25, per 1000 atoms: 0.12 Number of scatterers: 19560 At special positions: 0 Unit cell: (140.7, 138.02, 104.52, 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 130 16.00 O 3420 8.00 N 3250 7.00 C 12760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 146 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 155 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 155 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 155 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 155 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 155 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 155 " distance=2.04 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 146 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 146 " distance=2.04 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 146 " distance=2.04 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 146 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 146 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 146 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 146 " distance=2.04 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 146 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 744.0 milliseconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR A 51 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.781A pdb=" N SER A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR B 51 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.782A pdb=" N SER B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 37 Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR C 51 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.782A pdb=" N SER C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.734A pdb=" N ALA C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 37 Processing helix chain 'D' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR D 51 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.781A pdb=" N SER D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 121 removed outlier: 5.548A pdb=" N ALA D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 37 Processing helix chain 'E' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR E 51 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.781A pdb=" N SER E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 removed outlier: 5.548A pdb=" N ALA E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 131 through 139 removed outlier: 3.732A pdb=" N ALA E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS E 168 " --> pdb=" O GLN E 164 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 186 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 260 Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS E 278 " --> pdb=" O SER E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 37 Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR F 51 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.781A pdb=" N SER F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 150 removed outlier: 4.127A pdb=" N GLU F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing helix chain 'F' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS F 168 " --> pdb=" O GLN F 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 186 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 Processing helix chain 'F' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS F 278 " --> pdb=" O SER F 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 37 Processing helix chain 'G' and resid 47 through 71 removed outlier: 3.834A pdb=" N TYR G 51 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.781A pdb=" N SER G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS G 168 " --> pdb=" O GLN G 164 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP G 169 " --> pdb=" O ASP G 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 186 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 260 Processing helix chain 'G' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 37 Processing helix chain 'H' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR H 51 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.781A pdb=" N SER H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU H 77 " --> pdb=" O ARG H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 153 No H-bonds generated for 'chain 'H' and resid 151 through 153' Processing helix chain 'H' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP H 169 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE H 186 " --> pdb=" O ILE H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE H 209 " --> pdb=" O LEU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 260 Processing helix chain 'H' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS H 278 " --> pdb=" O SER H 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 37 Processing helix chain 'I' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR I 51 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix removed outlier: 3.781A pdb=" N SER I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU I 77 " --> pdb=" O ARG I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 131 through 139 removed outlier: 3.734A pdb=" N ALA I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 153 No H-bonds generated for 'chain 'I' and resid 151 through 153' Processing helix chain 'I' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE I 186 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 260 Processing helix chain 'I' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS I 278 " --> pdb=" O SER I 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 37 Processing helix chain 'J' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR J 51 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix removed outlier: 3.781A pdb=" N SER J 71 " --> pdb=" O GLY J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU J 77 " --> pdb=" O ARG J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 121 through 127 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'J' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS J 168 " --> pdb=" O GLN J 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE J 186 " --> pdb=" O ILE J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE J 209 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 260 Processing helix chain 'J' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS J 278 " --> pdb=" O SER J 274 " (cutoff:3.500A) 1311 hydrogen bonds defined for protein. 3933 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: 2.94 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6040 1.34 - 1.46: 4782 1.46 - 1.58: 9038 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 20010 Sorted by residual: bond pdb=" C LEU I 150 " pdb=" N PRO I 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C LEU B 150 " pdb=" N PRO B 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.98e-01 bond pdb=" C LEU J 150 " pdb=" N PRO J 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.90e-01 bond pdb=" C LEU H 150 " pdb=" N PRO H 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.89e-01 bond pdb=" C LEU E 150 " pdb=" N PRO E 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.79e-01 ... (remaining 20005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 26432 1.92 - 3.84: 588 3.84 - 5.77: 150 5.77 - 7.69: 20 7.69 - 9.61: 10 Bond angle restraints: 27200 Sorted by residual: angle pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " pdb=" CG LEU A 190 " ideal model delta sigma weight residual 116.30 106.69 9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 106.69 9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU J 190 " pdb=" CB LEU J 190 " pdb=" CG LEU J 190 " ideal model delta sigma weight residual 116.30 106.70 9.60 3.50e+00 8.16e-02 7.52e+00 angle pdb=" CA LEU D 190 " pdb=" CB LEU D 190 " pdb=" CG LEU D 190 " ideal model delta sigma weight residual 116.30 106.71 9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CA LEU G 190 " pdb=" CB LEU G 190 " pdb=" CG LEU G 190 " ideal model delta sigma weight residual 116.30 106.71 9.59 3.50e+00 8.16e-02 7.51e+00 ... (remaining 27195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 10562 17.73 - 35.46: 1128 35.46 - 53.19: 200 53.19 - 70.93: 20 70.93 - 88.66: 20 Dihedral angle restraints: 11930 sinusoidal: 4570 harmonic: 7360 Sorted by residual: dihedral pdb=" CB CYS E 43 " pdb=" SG CYS E 43 " pdb=" SG CYS E 155 " pdb=" CB CYS E 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.20 -65.80 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS J 43 " pdb=" SG CYS J 43 " pdb=" SG CYS J 155 " pdb=" CB CYS J 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.21 -65.79 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 155 " pdb=" CB CYS C 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.22 -65.78 1 1.00e+01 1.00e-02 5.66e+01 ... (remaining 11927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2561 0.051 - 0.102: 557 0.102 - 0.153: 42 0.153 - 0.203: 0 0.203 - 0.254: 10 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CG LEU C 190 " pdb=" CB LEU C 190 " pdb=" CD1 LEU C 190 " pdb=" CD2 LEU C 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU E 190 " pdb=" CB LEU E 190 " pdb=" CD1 LEU E 190 " pdb=" CD2 LEU E 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU G 190 " pdb=" CB LEU G 190 " pdb=" CD1 LEU G 190 " pdb=" CD2 LEU G 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3167 not shown) Planarity restraints: 3350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 173 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLN F 173 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN F 173 " -0.012 2.00e-02 2.50e+03 pdb=" N SER F 174 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 173 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C GLN H 173 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN H 173 " 0.012 2.00e-02 2.50e+03 pdb=" N SER H 174 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 173 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLN A 173 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN A 173 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 174 " 0.011 2.00e-02 2.50e+03 ... (remaining 3347 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1407 2.73 - 3.27: 22326 3.27 - 3.81: 31951 3.81 - 4.36: 34735 4.36 - 4.90: 57513 Nonbonded interactions: 147932 Sorted by model distance: nonbonded pdb=" O PRO C 42 " pdb=" ND2 ASN C 48 " model vdw 2.183 3.120 nonbonded pdb=" O PRO I 42 " pdb=" ND2 ASN I 48 " model vdw 2.184 3.120 nonbonded pdb=" O PRO D 42 " pdb=" ND2 ASN D 48 " model vdw 2.184 3.120 nonbonded pdb=" O PRO G 42 " pdb=" ND2 ASN G 48 " model vdw 2.184 3.120 nonbonded pdb=" O PRO H 42 " pdb=" ND2 ASN H 48 " model vdw 2.184 3.120 ... (remaining 147927 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.230 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 14.850 Find NCS groups from input model: 0.160 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.004 0.036 20040 Z= 0.201 Angle : 0.780 9.611 27260 Z= 0.414 Chirality : 0.043 0.254 3170 Planarity : 0.005 0.031 3350 Dihedral : 14.562 88.658 7080 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.05 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.16), residues: 2480 helix: -0.63 (0.11), residues: 1880 sheet: None (None), residues: 0 loop : -3.55 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 32 TYR 0.014 0.002 TYR A 68 PHE 0.018 0.002 PHE I 266 TRP 0.029 0.002 TRP J 113 HIS 0.004 0.002 HIS H 277 Details of bonding type rmsd covalent geometry : bond 0.00426 (20010) covalent geometry : angle 0.77914 (27200) SS BOND : bond 0.00523 ( 30) SS BOND : angle 1.13403 ( 60) hydrogen bonds : bond 0.09419 ( 1311) hydrogen bonds : angle 6.04204 ( 3933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 785 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7016 (ttt-90) cc_final: 0.6343 (tpt170) REVERT: A 111 LEU cc_start: 0.8362 (mt) cc_final: 0.8116 (mt) REVERT: A 197 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7566 (mtt90) REVERT: A 215 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8335 (tp30) REVERT: A 231 GLU cc_start: 0.8624 (pp20) cc_final: 0.8249 (pp20) REVERT: A 234 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7543 (ttpt) REVERT: A 235 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8335 (tm-30) REVERT: A 236 ASN cc_start: 0.8036 (m110) cc_final: 0.7561 (m110) REVERT: A 256 GLU cc_start: 0.8374 (tt0) cc_final: 0.8047 (tt0) REVERT: B 32 ARG cc_start: 0.6573 (ttt-90) cc_final: 0.6160 (tpt170) REVERT: B 73 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7691 (tpp-160) REVERT: B 197 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7532 (mtt90) REVERT: B 215 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 231 GLU cc_start: 0.8658 (pp20) cc_final: 0.8230 (pp20) REVERT: B 234 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7705 (ttpt) REVERT: B 235 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 236 ASN cc_start: 0.8286 (m110) cc_final: 0.7640 (m-40) REVERT: C 51 TYR cc_start: 0.8813 (t80) cc_final: 0.8540 (t80) REVERT: C 55 PHE cc_start: 0.8550 (m-80) cc_final: 0.7842 (m-80) REVERT: C 73 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7629 (tpp-160) REVERT: C 94 ARG cc_start: 0.4800 (ttm110) cc_final: 0.4539 (ptt180) REVERT: C 231 GLU cc_start: 0.8697 (pp20) cc_final: 0.8386 (pp20) REVERT: C 234 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7833 (ttpt) REVERT: C 235 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 236 ASN cc_start: 0.8328 (m110) cc_final: 0.7944 (m110) REVERT: D 32 ARG cc_start: 0.6392 (ttt-90) cc_final: 0.6087 (tpt170) REVERT: D 125 GLU cc_start: 0.7591 (tp30) cc_final: 0.7144 (tp30) REVERT: D 189 LEU cc_start: 0.8623 (tt) cc_final: 0.8196 (tp) REVERT: D 198 CYS cc_start: 0.9041 (t) cc_final: 0.8758 (t) REVERT: D 208 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8073 (mtmt) REVERT: D 231 GLU cc_start: 0.8558 (pp20) cc_final: 0.8350 (pp20) REVERT: D 234 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7753 (ttpt) REVERT: D 236 ASN cc_start: 0.8286 (m110) cc_final: 0.7951 (m-40) REVERT: D 279 TYR cc_start: 0.7605 (t80) cc_final: 0.7331 (t80) REVERT: D 282 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.6932 (mmm160) REVERT: E 32 ARG cc_start: 0.7334 (ttt-90) cc_final: 0.6948 (tpp-160) REVERT: E 73 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7522 (tpp-160) REVERT: E 94 ARG cc_start: 0.5258 (ttm110) cc_final: 0.4883 (ptt180) REVERT: E 231 GLU cc_start: 0.8513 (pp20) cc_final: 0.7896 (pp20) REVERT: E 234 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7751 (tttt) REVERT: E 235 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8237 (tm-30) REVERT: E 236 ASN cc_start: 0.7996 (m110) cc_final: 0.7607 (m110) REVERT: E 282 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6765 (mmm160) REVERT: F 32 ARG cc_start: 0.6948 (ttt-90) cc_final: 0.6391 (tpt170) REVERT: F 94 ARG cc_start: 0.5099 (ttm110) cc_final: 0.4839 (ptt180) REVERT: F 166 LEU cc_start: 0.8220 (tt) cc_final: 0.7482 (mt) REVERT: F 197 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7726 (mtt90) REVERT: F 231 GLU cc_start: 0.8756 (pp20) cc_final: 0.8289 (pp20) REVERT: F 234 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7513 (tttt) REVERT: F 235 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8284 (tm-30) REVERT: F 236 ASN cc_start: 0.8175 (m110) cc_final: 0.7706 (m110) REVERT: F 256 GLU cc_start: 0.8321 (tt0) cc_final: 0.8041 (tt0) REVERT: G 32 ARG cc_start: 0.6886 (ttt-90) cc_final: 0.6518 (tpt170) REVERT: G 73 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7422 (tpp-160) REVERT: G 134 PHE cc_start: 0.8455 (t80) cc_final: 0.8061 (t80) REVERT: G 236 ASN cc_start: 0.8046 (m110) cc_final: 0.7442 (m-40) REVERT: H 73 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7608 (tpp-160) REVERT: H 94 ARG cc_start: 0.4815 (ttm110) cc_final: 0.4529 (ptt180) REVERT: H 215 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8304 (tm-30) REVERT: H 220 ILE cc_start: 0.8378 (mm) cc_final: 0.8018 (mm) REVERT: H 234 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7689 (tttt) REVERT: H 236 ASN cc_start: 0.7913 (m110) cc_final: 0.7545 (m-40) REVERT: H 258 GLN cc_start: 0.7808 (tt0) cc_final: 0.7575 (tm-30) REVERT: I 32 ARG cc_start: 0.6662 (ttt-90) cc_final: 0.6306 (tpt170) REVERT: I 208 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8128 (mtpt) REVERT: I 231 GLU cc_start: 0.8436 (pp20) cc_final: 0.7975 (pp20) REVERT: I 234 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7699 (ttpt) REVERT: I 236 ASN cc_start: 0.8332 (m110) cc_final: 0.8036 (m-40) REVERT: I 282 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.6789 (mmm160) REVERT: J 32 ARG cc_start: 0.7135 (ttt-90) cc_final: 0.6894 (ttt90) REVERT: J 73 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7379 (tpp-160) REVERT: J 94 ARG cc_start: 0.5394 (ttm110) cc_final: 0.4810 (ptt180) REVERT: J 205 LEU cc_start: 0.9264 (tp) cc_final: 0.9044 (tp) REVERT: J 217 GLU cc_start: 0.7728 (tt0) cc_final: 0.7474 (tt0) REVERT: J 231 GLU cc_start: 0.8510 (pp20) cc_final: 0.7979 (pp20) REVERT: J 234 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7549 (tttt) REVERT: J 235 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7945 (tm-30) REVERT: J 236 ASN cc_start: 0.8040 (m110) cc_final: 0.7543 (m110) REVERT: J 282 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.6852 (mmm160) outliers start: 0 outliers final: 0 residues processed: 785 average time/residue: 0.1425 time to fit residues: 166.2599 Evaluate side-chains 637 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 216 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 245 HIS B 277 HIS ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS D 175 GLN D 216 GLN D 277 HIS E 216 GLN E 258 GLN E 277 HIS ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN F 277 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 GLN G 277 HIS H 175 GLN H 216 GLN H 277 HIS I 175 GLN I 216 GLN I 258 GLN I 277 HIS J 216 GLN J 258 GLN J 277 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116370 restraints weight = 35250.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119608 restraints weight = 20863.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121872 restraints weight = 13916.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123397 restraints weight = 10141.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124696 restraints weight = 7979.247| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20040 Z= 0.152 Angle : 0.715 6.927 27260 Z= 0.363 Chirality : 0.041 0.195 3170 Planarity : 0.005 0.044 3350 Dihedral : 5.293 24.059 2690 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2480 helix: 0.62 (0.12), residues: 1840 sheet: None (None), residues: 0 loop : -3.29 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 144 TYR 0.021 0.002 TYR G 279 PHE 0.015 0.002 PHE H 204 TRP 0.016 0.001 TRP J 113 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00324 (20010) covalent geometry : angle 0.71047 (27200) SS BOND : bond 0.00251 ( 30) SS BOND : angle 1.77078 ( 60) hydrogen bonds : bond 0.04534 ( 1311) hydrogen bonds : angle 4.69785 ( 3933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 753 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7725 (tp30) cc_final: 0.7441 (tp30) REVERT: A 215 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8182 (tp30) REVERT: A 219 GLN cc_start: 0.7541 (tm-30) cc_final: 0.6984 (tm-30) REVERT: A 220 ILE cc_start: 0.8876 (tt) cc_final: 0.8377 (tt) REVERT: A 234 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7532 (ttpt) REVERT: A 235 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 236 ASN cc_start: 0.7881 (m110) cc_final: 0.7548 (m-40) REVERT: A 258 GLN cc_start: 0.8028 (tt0) cc_final: 0.7796 (tm-30) REVERT: B 32 ARG cc_start: 0.6453 (ttt-90) cc_final: 0.6157 (tpt170) REVERT: B 125 GLU cc_start: 0.7703 (tp30) cc_final: 0.7253 (tp30) REVERT: B 215 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8030 (tp30) REVERT: B 231 GLU cc_start: 0.8451 (pp20) cc_final: 0.8110 (pp20) REVERT: B 234 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7719 (tttm) REVERT: B 235 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 236 ASN cc_start: 0.7957 (m110) cc_final: 0.7538 (m-40) REVERT: B 278 LYS cc_start: 0.8507 (tttt) cc_final: 0.8252 (ttpt) REVERT: C 94 ARG cc_start: 0.5216 (ttm110) cc_final: 0.4958 (ptt180) REVERT: C 125 GLU cc_start: 0.7706 (tp30) cc_final: 0.7408 (tp30) REVERT: C 234 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7836 (ttpt) REVERT: C 235 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8249 (tm-30) REVERT: C 236 ASN cc_start: 0.8064 (m110) cc_final: 0.7791 (m-40) REVERT: C 258 GLN cc_start: 0.8291 (tt0) cc_final: 0.7883 (tm-30) REVERT: D 32 ARG cc_start: 0.6500 (ttt-90) cc_final: 0.6228 (tpt170) REVERT: D 125 GLU cc_start: 0.7720 (tp30) cc_final: 0.7432 (tp30) REVERT: D 189 LEU cc_start: 0.8696 (tt) cc_final: 0.8318 (tp) REVERT: D 192 PHE cc_start: 0.8821 (t80) cc_final: 0.8597 (t80) REVERT: D 234 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7788 (ttpt) REVERT: D 267 ASN cc_start: 0.8338 (t0) cc_final: 0.7835 (t0) REVERT: D 282 ARG cc_start: 0.7263 (mtm-85) cc_final: 0.6753 (mmm160) REVERT: E 32 ARG cc_start: 0.7245 (ttt-90) cc_final: 0.6751 (tpp-160) REVERT: E 73 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7662 (tpp-160) REVERT: E 125 GLU cc_start: 0.7497 (tp30) cc_final: 0.7262 (tp30) REVERT: E 231 GLU cc_start: 0.8510 (pp20) cc_final: 0.8256 (tm-30) REVERT: E 234 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7680 (tttt) REVERT: E 235 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8199 (tm-30) REVERT: E 236 ASN cc_start: 0.7770 (m110) cc_final: 0.7496 (m110) REVERT: F 32 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6897 (ttt90) REVERT: F 94 ARG cc_start: 0.5202 (ttm110) cc_final: 0.4878 (ptt180) REVERT: F 125 GLU cc_start: 0.7803 (tp30) cc_final: 0.7359 (tp30) REVERT: F 166 LEU cc_start: 0.8061 (tt) cc_final: 0.7440 (mt) REVERT: F 219 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7117 (tm-30) REVERT: F 220 ILE cc_start: 0.8860 (tt) cc_final: 0.8342 (tt) REVERT: F 234 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7578 (ttpt) REVERT: F 235 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8196 (tm-30) REVERT: F 236 ASN cc_start: 0.7948 (m110) cc_final: 0.7652 (m-40) REVERT: F 256 GLU cc_start: 0.8068 (tt0) cc_final: 0.7776 (tt0) REVERT: F 258 GLN cc_start: 0.8048 (tt0) cc_final: 0.7837 (tm-30) REVERT: G 32 ARG cc_start: 0.6562 (ttt-90) cc_final: 0.6152 (tpt170) REVERT: G 125 GLU cc_start: 0.7640 (tp30) cc_final: 0.7346 (tp30) REVERT: G 220 ILE cc_start: 0.8640 (tt) cc_final: 0.8348 (tt) REVERT: G 234 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7694 (ttpt) REVERT: G 235 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8227 (tm-30) REVERT: H 53 LEU cc_start: 0.8872 (tp) cc_final: 0.8651 (tp) REVERT: H 94 ARG cc_start: 0.5142 (ttm110) cc_final: 0.4705 (ptt180) REVERT: H 125 GLU cc_start: 0.7620 (tp30) cc_final: 0.7377 (tp30) REVERT: H 215 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8323 (tm-30) REVERT: H 234 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7655 (ttpt) REVERT: H 267 ASN cc_start: 0.8426 (t0) cc_final: 0.7841 (t0) REVERT: I 32 ARG cc_start: 0.6981 (ttt-90) cc_final: 0.6465 (tpt170) REVERT: I 51 TYR cc_start: 0.8944 (t80) cc_final: 0.8576 (t80) REVERT: I 125 GLU cc_start: 0.7842 (tp30) cc_final: 0.7641 (tp30) REVERT: I 208 LYS cc_start: 0.8339 (mtpp) cc_final: 0.8077 (mtmt) REVERT: I 224 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8014 (ttpt) REVERT: I 231 GLU cc_start: 0.8413 (pp20) cc_final: 0.8064 (pp20) REVERT: I 234 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7797 (ttpt) REVERT: I 256 GLU cc_start: 0.8213 (tt0) cc_final: 0.7941 (tt0) REVERT: I 267 ASN cc_start: 0.8506 (t0) cc_final: 0.7892 (t0) REVERT: I 279 TYR cc_start: 0.7960 (t80) cc_final: 0.7626 (t80) REVERT: J 32 ARG cc_start: 0.7105 (ttt-90) cc_final: 0.6849 (ttt90) REVERT: J 73 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7440 (tpp-160) REVERT: J 94 ARG cc_start: 0.5329 (ttm110) cc_final: 0.5096 (ptt180) REVERT: J 217 GLU cc_start: 0.7964 (tt0) cc_final: 0.7422 (tt0) REVERT: J 231 GLU cc_start: 0.8474 (pp20) cc_final: 0.8259 (tm-30) REVERT: J 234 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7629 (tttt) REVERT: J 282 ARG cc_start: 0.7002 (mtm-85) cc_final: 0.6750 (mmm160) outliers start: 0 outliers final: 0 residues processed: 753 average time/residue: 0.1216 time to fit residues: 141.2009 Evaluate side-chains 614 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 249 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 48 ASN B 175 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN F 206 GLN G 175 GLN H 175 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110424 restraints weight = 36923.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113507 restraints weight = 21952.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115691 restraints weight = 14801.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117197 restraints weight = 10951.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118431 restraints weight = 8696.140| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20040 Z= 0.296 Angle : 0.899 12.196 27260 Z= 0.456 Chirality : 0.047 0.279 3170 Planarity : 0.006 0.051 3350 Dihedral : 5.582 23.669 2690 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2480 helix: 0.16 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 144 TYR 0.033 0.003 TYR A 51 PHE 0.033 0.003 PHE C 55 TRP 0.023 0.002 TRP C 113 HIS 0.007 0.002 HIS H 277 Details of bonding type rmsd covalent geometry : bond 0.00648 (20010) covalent geometry : angle 0.89766 (27200) SS BOND : bond 0.00856 ( 30) SS BOND : angle 1.36625 ( 60) hydrogen bonds : bond 0.05491 ( 1311) hydrogen bonds : angle 5.12817 ( 3933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 704 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8977 (t80) cc_final: 0.8743 (t80) REVERT: A 63 LEU cc_start: 0.8880 (tp) cc_final: 0.8665 (tp) REVERT: A 166 LEU cc_start: 0.8169 (tt) cc_final: 0.7420 (mt) REVERT: A 215 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8347 (tp30) REVERT: A 220 ILE cc_start: 0.8751 (tt) cc_final: 0.8503 (tt) REVERT: A 234 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7634 (ttpt) REVERT: A 235 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 236 ASN cc_start: 0.7763 (m110) cc_final: 0.7374 (m-40) REVERT: A 267 ASN cc_start: 0.8323 (t0) cc_final: 0.8081 (t0) REVERT: A 278 LYS cc_start: 0.8083 (tttt) cc_final: 0.7812 (ttpt) REVERT: B 32 ARG cc_start: 0.6650 (ttt-90) cc_final: 0.6105 (tpt170) REVERT: B 73 ARG cc_start: 0.4900 (tpp-160) cc_final: 0.3898 (tpt170) REVERT: B 125 GLU cc_start: 0.7772 (tp30) cc_final: 0.7335 (tp30) REVERT: B 166 LEU cc_start: 0.8376 (tt) cc_final: 0.7658 (mt) REVERT: B 197 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7730 (mtm-85) REVERT: B 205 LEU cc_start: 0.9217 (tp) cc_final: 0.8836 (tp) REVERT: B 215 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 234 LYS cc_start: 0.8350 (ttmt) cc_final: 0.7724 (tttm) REVERT: B 236 ASN cc_start: 0.7575 (m110) cc_final: 0.7325 (m-40) REVERT: B 278 LYS cc_start: 0.8510 (tttt) cc_final: 0.8133 (ttpt) REVERT: B 281 ASN cc_start: 0.7636 (p0) cc_final: 0.7369 (p0) REVERT: C 94 ARG cc_start: 0.5220 (ttm110) cc_final: 0.4721 (ptt180) REVERT: C 125 GLU cc_start: 0.7874 (tp30) cc_final: 0.7650 (tp30) REVERT: C 166 LEU cc_start: 0.8401 (tt) cc_final: 0.7768 (mt) REVERT: C 197 ARG cc_start: 0.8395 (mmt90) cc_final: 0.8175 (mtm-85) REVERT: C 205 LEU cc_start: 0.9079 (tp) cc_final: 0.8813 (tp) REVERT: C 220 ILE cc_start: 0.8727 (tt) cc_final: 0.8382 (tt) REVERT: C 231 GLU cc_start: 0.8573 (pp20) cc_final: 0.8240 (pp20) REVERT: C 234 LYS cc_start: 0.8582 (ttmt) cc_final: 0.7915 (ttpt) REVERT: C 236 ASN cc_start: 0.8111 (m110) cc_final: 0.7735 (m110) REVERT: C 267 ASN cc_start: 0.8278 (t0) cc_final: 0.7957 (t0) REVERT: C 278 LYS cc_start: 0.8501 (tttt) cc_final: 0.8250 (ttpt) REVERT: D 51 TYR cc_start: 0.9017 (t80) cc_final: 0.8716 (t80) REVERT: D 125 GLU cc_start: 0.7777 (tp30) cc_final: 0.7443 (tp30) REVERT: D 166 LEU cc_start: 0.8331 (tt) cc_final: 0.7616 (mt) REVERT: D 205 LEU cc_start: 0.9238 (tp) cc_final: 0.8867 (tp) REVERT: D 234 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7735 (tttt) REVERT: D 235 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8017 (tm-30) REVERT: D 267 ASN cc_start: 0.8310 (t0) cc_final: 0.7833 (t0) REVERT: E 32 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.6831 (ttm-80) REVERT: E 53 LEU cc_start: 0.8711 (tp) cc_final: 0.8509 (tp) REVERT: E 73 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7519 (tpp-160) REVERT: E 118 LEU cc_start: 0.8730 (tp) cc_final: 0.8448 (tp) REVERT: E 125 GLU cc_start: 0.7938 (tp30) cc_final: 0.7647 (tp30) REVERT: E 144 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8118 (tmm-80) REVERT: E 166 LEU cc_start: 0.8446 (tt) cc_final: 0.7685 (mt) REVERT: E 205 LEU cc_start: 0.9206 (tp) cc_final: 0.8887 (tp) REVERT: E 234 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7910 (tttt) REVERT: E 278 LYS cc_start: 0.8533 (tttt) cc_final: 0.8300 (ttmt) REVERT: F 32 ARG cc_start: 0.7234 (ttt-90) cc_final: 0.6875 (ttt90) REVERT: F 51 TYR cc_start: 0.8868 (t80) cc_final: 0.8514 (t80) REVERT: F 63 LEU cc_start: 0.8856 (tp) cc_final: 0.8653 (tp) REVERT: F 125 GLU cc_start: 0.7749 (tp30) cc_final: 0.7380 (tp30) REVERT: F 166 LEU cc_start: 0.8184 (tt) cc_final: 0.7567 (mt) REVERT: F 220 ILE cc_start: 0.8938 (tt) cc_final: 0.8718 (tt) REVERT: F 234 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7531 (ttpt) REVERT: F 267 ASN cc_start: 0.8370 (t0) cc_final: 0.7972 (t0) REVERT: F 278 LYS cc_start: 0.8109 (tttt) cc_final: 0.7848 (ttmt) REVERT: G 32 ARG cc_start: 0.6748 (ttt-90) cc_final: 0.6262 (tpt170) REVERT: G 73 ARG cc_start: 0.4897 (tpp-160) cc_final: 0.4097 (tpt170) REVERT: G 125 GLU cc_start: 0.7712 (tp30) cc_final: 0.7286 (tp30) REVERT: G 173 GLN cc_start: 0.8898 (mt0) cc_final: 0.7936 (mp10) REVERT: G 234 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7592 (ttpt) REVERT: G 281 ASN cc_start: 0.7527 (p0) cc_final: 0.7188 (p0) REVERT: H 32 ARG cc_start: 0.6558 (ttt-90) cc_final: 0.6021 (tpt170) REVERT: H 94 ARG cc_start: 0.5354 (ttm110) cc_final: 0.4661 (ptt180) REVERT: H 125 GLU cc_start: 0.7708 (tp30) cc_final: 0.7378 (tp30) REVERT: H 144 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8120 (tmm-80) REVERT: H 173 GLN cc_start: 0.8976 (mt0) cc_final: 0.8658 (mt0) REVERT: H 234 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7727 (ttpt) REVERT: H 267 ASN cc_start: 0.8366 (t0) cc_final: 0.8040 (t0) REVERT: H 278 LYS cc_start: 0.8327 (tttt) cc_final: 0.8015 (ttpt) REVERT: I 32 ARG cc_start: 0.6906 (ttt-90) cc_final: 0.6539 (tpt170) REVERT: I 73 ARG cc_start: 0.5774 (tpp-160) cc_final: 0.4585 (tpt170) REVERT: I 111 LEU cc_start: 0.8451 (mt) cc_final: 0.8206 (mt) REVERT: I 125 GLU cc_start: 0.7777 (tp30) cc_final: 0.7577 (tp30) REVERT: I 205 LEU cc_start: 0.9250 (tp) cc_final: 0.8791 (tp) REVERT: I 208 LYS cc_start: 0.8463 (mtpp) cc_final: 0.7933 (mtpt) REVERT: I 215 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8235 (tp30) REVERT: I 234 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7683 (tttt) REVERT: I 235 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7901 (tm-30) REVERT: I 267 ASN cc_start: 0.8477 (t0) cc_final: 0.8032 (t0) REVERT: J 32 ARG cc_start: 0.7304 (ttt-90) cc_final: 0.6808 (ttt90) REVERT: J 51 TYR cc_start: 0.8886 (t80) cc_final: 0.8677 (t80) REVERT: J 73 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7525 (tpp-160) REVERT: J 94 ARG cc_start: 0.5344 (ttm110) cc_final: 0.4882 (ptt180) REVERT: J 118 LEU cc_start: 0.8564 (tp) cc_final: 0.8287 (tp) REVERT: J 144 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8312 (tmm-80) REVERT: J 166 LEU cc_start: 0.8348 (tt) cc_final: 0.7559 (mt) REVERT: J 197 ARG cc_start: 0.8668 (mtt90) cc_final: 0.7974 (mtt90) REVERT: J 205 LEU cc_start: 0.9207 (tp) cc_final: 0.8935 (tp) REVERT: J 234 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7746 (tttt) REVERT: J 235 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7728 (tm-30) REVERT: J 267 ASN cc_start: 0.8309 (t0) cc_final: 0.8099 (t0) outliers start: 1 outliers final: 0 residues processed: 705 average time/residue: 0.1349 time to fit residues: 145.0349 Evaluate side-chains 600 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 210 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 235 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN C 245 HIS ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN I 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116997 restraints weight = 35821.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120258 restraints weight = 21357.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122577 restraints weight = 14272.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124282 restraints weight = 10342.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125388 restraints weight = 8009.074| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20040 Z= 0.170 Angle : 0.753 9.459 27260 Z= 0.379 Chirality : 0.042 0.197 3170 Planarity : 0.005 0.047 3350 Dihedral : 5.296 24.085 2690 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2480 helix: 0.53 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 144 TYR 0.031 0.002 TYR I 51 PHE 0.016 0.002 PHE H 55 TRP 0.019 0.001 TRP D 113 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00374 (20010) covalent geometry : angle 0.74971 (27200) SS BOND : bond 0.00402 ( 30) SS BOND : angle 1.69259 ( 60) hydrogen bonds : bond 0.04663 ( 1311) hydrogen bonds : angle 4.70552 ( 3933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 745 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8668 (t80) cc_final: 0.8182 (t80) REVERT: A 73 ARG cc_start: 0.6321 (mmp-170) cc_final: 0.5542 (tpp80) REVERT: A 166 LEU cc_start: 0.8219 (tt) cc_final: 0.7610 (mt) REVERT: A 215 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8214 (tp30) REVERT: A 219 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 220 ILE cc_start: 0.8785 (tt) cc_final: 0.8541 (tt) REVERT: A 234 LYS cc_start: 0.8368 (ttmt) cc_final: 0.7662 (ttpt) REVERT: A 235 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 236 ASN cc_start: 0.7791 (m110) cc_final: 0.7524 (m110) REVERT: A 258 GLN cc_start: 0.8175 (tt0) cc_final: 0.7877 (tm-30) REVERT: A 267 ASN cc_start: 0.8196 (t0) cc_final: 0.7772 (t0) REVERT: B 32 ARG cc_start: 0.6583 (ttt-90) cc_final: 0.6100 (tpt170) REVERT: B 125 GLU cc_start: 0.7646 (tp30) cc_final: 0.7276 (tp30) REVERT: B 215 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8323 (tm-30) REVERT: B 234 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7695 (tttm) REVERT: B 278 LYS cc_start: 0.8367 (tttt) cc_final: 0.7928 (ttpt) REVERT: C 63 LEU cc_start: 0.8896 (tp) cc_final: 0.8679 (tp) REVERT: C 73 ARG cc_start: 0.6066 (mmp-170) cc_final: 0.5626 (tpp-160) REVERT: C 94 ARG cc_start: 0.5349 (ttm110) cc_final: 0.4699 (ptt180) REVERT: C 125 GLU cc_start: 0.7597 (tp30) cc_final: 0.7376 (tp30) REVERT: C 166 LEU cc_start: 0.8163 (tt) cc_final: 0.7605 (mt) REVERT: C 173 GLN cc_start: 0.8912 (mt0) cc_final: 0.8565 (mt0) REVERT: C 177 LEU cc_start: 0.9088 (tp) cc_final: 0.8736 (tp) REVERT: C 205 LEU cc_start: 0.8985 (tp) cc_final: 0.8649 (tp) REVERT: C 220 ILE cc_start: 0.8569 (tt) cc_final: 0.8169 (tt) REVERT: C 234 LYS cc_start: 0.8558 (ttmt) cc_final: 0.7865 (ttpt) REVERT: C 267 ASN cc_start: 0.8094 (t0) cc_final: 0.7595 (t0) REVERT: C 279 TYR cc_start: 0.7796 (t80) cc_final: 0.7446 (t80) REVERT: D 51 TYR cc_start: 0.8912 (t80) cc_final: 0.8519 (t80) REVERT: D 63 LEU cc_start: 0.8934 (tp) cc_final: 0.8711 (tp) REVERT: D 125 GLU cc_start: 0.7844 (tp30) cc_final: 0.7523 (tp30) REVERT: D 126 CYS cc_start: 0.6866 (t) cc_final: 0.6594 (t) REVERT: D 173 GLN cc_start: 0.8893 (mt0) cc_final: 0.7778 (mp10) REVERT: D 205 LEU cc_start: 0.9164 (tp) cc_final: 0.8685 (tp) REVERT: D 231 GLU cc_start: 0.8326 (pp20) cc_final: 0.8089 (pp20) REVERT: D 234 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7723 (tttt) REVERT: D 267 ASN cc_start: 0.8460 (t0) cc_final: 0.7960 (t0) REVERT: E 32 ARG cc_start: 0.7359 (ttt-90) cc_final: 0.6781 (tpp-160) REVERT: E 73 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7571 (tpp-160) REVERT: E 125 GLU cc_start: 0.7634 (tp30) cc_final: 0.7349 (tp30) REVERT: E 144 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8193 (ttp80) REVERT: E 166 LEU cc_start: 0.8237 (tt) cc_final: 0.7657 (mt) REVERT: E 173 GLN cc_start: 0.8763 (mt0) cc_final: 0.7973 (mp10) REVERT: E 205 LEU cc_start: 0.9124 (tp) cc_final: 0.8708 (tp) REVERT: E 234 LYS cc_start: 0.8379 (ttmt) cc_final: 0.7656 (tttt) REVERT: E 279 TYR cc_start: 0.7898 (t80) cc_final: 0.7674 (t80) REVERT: F 32 ARG cc_start: 0.6858 (ttt-90) cc_final: 0.6657 (ttt90) REVERT: F 63 LEU cc_start: 0.8870 (tp) cc_final: 0.8615 (tp) REVERT: F 125 GLU cc_start: 0.7683 (tp30) cc_final: 0.7336 (tp30) REVERT: F 166 LEU cc_start: 0.8023 (tt) cc_final: 0.7587 (mt) REVERT: F 173 GLN cc_start: 0.8430 (mt0) cc_final: 0.7502 (mp10) REVERT: F 219 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7174 (tm-30) REVERT: F 220 ILE cc_start: 0.8976 (tt) cc_final: 0.8526 (tt) REVERT: F 234 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7457 (ttpt) REVERT: F 235 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8295 (tm-30) REVERT: F 236 ASN cc_start: 0.7620 (m110) cc_final: 0.6829 (m110) REVERT: F 258 GLN cc_start: 0.8205 (tt0) cc_final: 0.7857 (tm-30) REVERT: G 32 ARG cc_start: 0.6452 (ttt-90) cc_final: 0.6157 (tpt170) REVERT: G 51 TYR cc_start: 0.8945 (t80) cc_final: 0.8661 (t80) REVERT: G 125 GLU cc_start: 0.7643 (tp30) cc_final: 0.7101 (tp30) REVERT: G 166 LEU cc_start: 0.8219 (tt) cc_final: 0.7459 (mt) REVERT: G 219 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7150 (tm-30) REVERT: G 220 ILE cc_start: 0.8626 (tt) cc_final: 0.8073 (tt) REVERT: G 224 LYS cc_start: 0.8602 (ttmt) cc_final: 0.7933 (ttpt) REVERT: G 234 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7607 (tttm) REVERT: G 281 ASN cc_start: 0.7577 (p0) cc_final: 0.7223 (p0) REVERT: H 32 ARG cc_start: 0.6745 (ttt-90) cc_final: 0.5932 (tpt170) REVERT: H 73 ARG cc_start: 0.6335 (mmp-170) cc_final: 0.5888 (tpp-160) REVERT: H 94 ARG cc_start: 0.5246 (ttm110) cc_final: 0.4601 (ptt180) REVERT: H 125 GLU cc_start: 0.7664 (tp30) cc_final: 0.7309 (tp30) REVERT: H 144 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8138 (tmm-80) REVERT: H 166 LEU cc_start: 0.8415 (tt) cc_final: 0.7758 (mt) REVERT: H 220 ILE cc_start: 0.8572 (tt) cc_final: 0.8284 (tt) REVERT: H 231 GLU cc_start: 0.8385 (pp20) cc_final: 0.8151 (pp20) REVERT: H 234 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7612 (ttpt) REVERT: H 256 GLU cc_start: 0.8438 (tt0) cc_final: 0.8229 (tt0) REVERT: H 267 ASN cc_start: 0.8115 (t0) cc_final: 0.7658 (t0) REVERT: I 32 ARG cc_start: 0.6552 (ttt-90) cc_final: 0.6207 (tpt170) REVERT: I 41 CYS cc_start: 0.5309 (t) cc_final: 0.5106 (t) REVERT: I 51 TYR cc_start: 0.8876 (t80) cc_final: 0.8636 (t80) REVERT: I 73 ARG cc_start: 0.5490 (mmp-170) cc_final: 0.5159 (tpt170) REVERT: I 125 GLU cc_start: 0.7871 (tp30) cc_final: 0.7541 (tp30) REVERT: I 166 LEU cc_start: 0.8245 (tt) cc_final: 0.7692 (mt) REVERT: I 173 GLN cc_start: 0.8932 (mt0) cc_final: 0.7947 (mp10) REVERT: I 208 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8016 (mtmt) REVERT: I 224 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8274 (ttpt) REVERT: I 231 GLU cc_start: 0.8486 (pp20) cc_final: 0.8020 (pp20) REVERT: I 234 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7636 (tttt) REVERT: I 235 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7861 (tm-30) REVERT: I 236 ASN cc_start: 0.7970 (m110) cc_final: 0.7558 (m-40) REVERT: I 267 ASN cc_start: 0.8427 (t0) cc_final: 0.7858 (t0) REVERT: J 32 ARG cc_start: 0.7096 (ttt-90) cc_final: 0.6737 (ttt90) REVERT: J 73 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7515 (tpp-160) REVERT: J 94 ARG cc_start: 0.5312 (ttm110) cc_final: 0.4840 (ptt180) REVERT: J 118 LEU cc_start: 0.8520 (tp) cc_final: 0.8300 (tp) REVERT: J 144 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8293 (tmm-80) REVERT: J 166 LEU cc_start: 0.8115 (tt) cc_final: 0.7469 (mt) REVERT: J 173 GLN cc_start: 0.8764 (mt0) cc_final: 0.7865 (mp10) REVERT: J 205 LEU cc_start: 0.9085 (tp) cc_final: 0.8865 (tp) REVERT: J 231 GLU cc_start: 0.8284 (pp20) cc_final: 0.7898 (pp20) REVERT: J 234 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7635 (tttt) REVERT: J 236 ASN cc_start: 0.7686 (m110) cc_final: 0.7477 (m-40) REVERT: J 279 TYR cc_start: 0.7897 (t80) cc_final: 0.7688 (t80) outliers start: 1 outliers final: 0 residues processed: 746 average time/residue: 0.1263 time to fit residues: 145.1291 Evaluate side-chains 629 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 19 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN C 245 HIS D 236 ASN I 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119065 restraints weight = 35477.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122408 restraints weight = 21320.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124671 restraints weight = 14291.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126479 restraints weight = 10418.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127650 restraints weight = 8044.059| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20040 Z= 0.144 Angle : 0.728 8.310 27260 Z= 0.360 Chirality : 0.041 0.200 3170 Planarity : 0.005 0.046 3350 Dihedral : 5.064 24.261 2690 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2480 helix: 0.80 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.64 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 144 TYR 0.028 0.002 TYR I 51 PHE 0.018 0.002 PHE D 64 TRP 0.015 0.001 TRP F 113 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00312 (20010) covalent geometry : angle 0.72469 (27200) SS BOND : bond 0.00241 ( 30) SS BOND : angle 1.56217 ( 60) hydrogen bonds : bond 0.04290 ( 1311) hydrogen bonds : angle 4.45283 ( 3933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 753 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8648 (t80) cc_final: 0.8215 (t80) REVERT: A 73 ARG cc_start: 0.6372 (mmp-170) cc_final: 0.5495 (tpp80) REVERT: A 125 GLU cc_start: 0.7370 (tp30) cc_final: 0.7055 (tp30) REVERT: A 166 LEU cc_start: 0.8194 (tt) cc_final: 0.7690 (mt) REVERT: A 173 GLN cc_start: 0.8357 (mt0) cc_final: 0.7460 (mt0) REVERT: A 234 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7652 (ttpt) REVERT: A 235 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 236 ASN cc_start: 0.7825 (m110) cc_final: 0.7600 (m110) REVERT: B 32 ARG cc_start: 0.6575 (ttt-90) cc_final: 0.6110 (tpt170) REVERT: B 125 GLU cc_start: 0.7639 (tp30) cc_final: 0.7146 (tp30) REVERT: B 215 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 234 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7683 (ttpt) REVERT: B 278 LYS cc_start: 0.8303 (tttt) cc_final: 0.7683 (ttpt) REVERT: C 63 LEU cc_start: 0.8933 (tp) cc_final: 0.8696 (tp) REVERT: C 73 ARG cc_start: 0.6214 (mmp-170) cc_final: 0.5704 (tpp-160) REVERT: C 94 ARG cc_start: 0.5355 (ttm110) cc_final: 0.4678 (ptt180) REVERT: C 125 GLU cc_start: 0.7562 (tp30) cc_final: 0.7227 (tp30) REVERT: C 166 LEU cc_start: 0.8049 (tt) cc_final: 0.7527 (mt) REVERT: C 173 GLN cc_start: 0.8929 (mt0) cc_final: 0.8523 (mt0) REVERT: C 177 LEU cc_start: 0.8996 (tp) cc_final: 0.8622 (tp) REVERT: C 220 ILE cc_start: 0.8569 (tt) cc_final: 0.8119 (tt) REVERT: C 234 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7714 (ttpt) REVERT: C 267 ASN cc_start: 0.8301 (t0) cc_final: 0.7840 (t0) REVERT: D 125 GLU cc_start: 0.7692 (tp30) cc_final: 0.7342 (tp30) REVERT: D 173 GLN cc_start: 0.8925 (mt0) cc_final: 0.7805 (mp10) REVERT: D 231 GLU cc_start: 0.8373 (pp20) cc_final: 0.8023 (pp20) REVERT: D 234 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7783 (tttt) REVERT: D 267 ASN cc_start: 0.8439 (t0) cc_final: 0.7839 (t0) REVERT: D 279 TYR cc_start: 0.8032 (t80) cc_final: 0.7822 (t80) REVERT: E 32 ARG cc_start: 0.7336 (ttt-90) cc_final: 0.6767 (tpp-160) REVERT: E 73 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7502 (tpp-160) REVERT: E 144 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8147 (ttp80) REVERT: E 166 LEU cc_start: 0.8175 (tt) cc_final: 0.7564 (mt) REVERT: E 173 GLN cc_start: 0.8730 (mt0) cc_final: 0.8028 (mp10) REVERT: E 231 GLU cc_start: 0.8349 (pp20) cc_final: 0.8084 (tm-30) REVERT: E 234 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7708 (tttt) REVERT: E 235 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7885 (tm-30) REVERT: E 236 ASN cc_start: 0.7664 (m110) cc_final: 0.7395 (m-40) REVERT: E 279 TYR cc_start: 0.7863 (t80) cc_final: 0.7622 (t80) REVERT: F 32 ARG cc_start: 0.6976 (ttt-90) cc_final: 0.6732 (ttt90) REVERT: F 63 LEU cc_start: 0.8868 (tp) cc_final: 0.8577 (tp) REVERT: F 125 GLU cc_start: 0.7663 (tp30) cc_final: 0.7315 (tp30) REVERT: F 126 CYS cc_start: 0.6784 (t) cc_final: 0.6515 (t) REVERT: F 166 LEU cc_start: 0.7996 (tt) cc_final: 0.7539 (mt) REVERT: F 173 GLN cc_start: 0.8423 (mt0) cc_final: 0.7504 (mp10) REVERT: F 234 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7486 (ttpt) REVERT: F 235 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8354 (tm-30) REVERT: F 236 ASN cc_start: 0.7552 (m110) cc_final: 0.6920 (m110) REVERT: F 258 GLN cc_start: 0.8219 (tt0) cc_final: 0.7992 (tm-30) REVERT: G 32 ARG cc_start: 0.6833 (ttt-90) cc_final: 0.6289 (tpt170) REVERT: G 125 GLU cc_start: 0.7627 (tp30) cc_final: 0.7075 (tp30) REVERT: G 166 LEU cc_start: 0.8196 (tt) cc_final: 0.7558 (mt) REVERT: G 173 GLN cc_start: 0.8810 (mt0) cc_final: 0.7852 (mp10) REVERT: G 219 GLN cc_start: 0.7398 (tm-30) cc_final: 0.7133 (tm-30) REVERT: G 220 ILE cc_start: 0.8631 (tt) cc_final: 0.7947 (tt) REVERT: G 224 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7878 (ttpt) REVERT: G 234 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7670 (ttpt) REVERT: G 278 LYS cc_start: 0.8232 (tttt) cc_final: 0.7679 (ttmt) REVERT: H 32 ARG cc_start: 0.6813 (ttt-90) cc_final: 0.5902 (tpt170) REVERT: H 63 LEU cc_start: 0.8963 (tp) cc_final: 0.8761 (tp) REVERT: H 73 ARG cc_start: 0.6249 (mmp-170) cc_final: 0.5774 (tpp-160) REVERT: H 94 ARG cc_start: 0.5223 (ttm110) cc_final: 0.4577 (ptt180) REVERT: H 125 GLU cc_start: 0.7763 (tp30) cc_final: 0.7415 (tp30) REVERT: H 144 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8002 (tmm-80) REVERT: H 166 LEU cc_start: 0.8478 (tt) cc_final: 0.7846 (mt) REVERT: H 220 ILE cc_start: 0.8589 (tt) cc_final: 0.8187 (tt) REVERT: H 224 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7983 (ttpt) REVERT: H 234 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7612 (ttpt) REVERT: H 267 ASN cc_start: 0.8348 (t0) cc_final: 0.7821 (t0) REVERT: I 32 ARG cc_start: 0.6863 (ttt-90) cc_final: 0.6460 (tpt170) REVERT: I 63 LEU cc_start: 0.8915 (tp) cc_final: 0.8711 (tp) REVERT: I 73 ARG cc_start: 0.5354 (mmp-170) cc_final: 0.4929 (tpt170) REVERT: I 125 GLU cc_start: 0.7693 (tp30) cc_final: 0.7354 (tp30) REVERT: I 166 LEU cc_start: 0.8201 (tt) cc_final: 0.7650 (mt) REVERT: I 173 GLN cc_start: 0.8967 (mt0) cc_final: 0.8036 (mt0) REVERT: I 208 LYS cc_start: 0.8352 (mtpp) cc_final: 0.7969 (mtmt) REVERT: I 224 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8245 (ttpt) REVERT: I 231 GLU cc_start: 0.8364 (pp20) cc_final: 0.7920 (pp20) REVERT: I 234 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7633 (tttt) REVERT: I 267 ASN cc_start: 0.8419 (t0) cc_final: 0.7868 (t0) REVERT: I 279 TYR cc_start: 0.7987 (t80) cc_final: 0.7752 (t80) REVERT: J 32 ARG cc_start: 0.7259 (ttt-90) cc_final: 0.6698 (ttt90) REVERT: J 39 PHE cc_start: 0.8308 (t80) cc_final: 0.7976 (t80) REVERT: J 63 LEU cc_start: 0.8985 (tp) cc_final: 0.8762 (tp) REVERT: J 73 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7456 (tpp-160) REVERT: J 94 ARG cc_start: 0.5136 (ttm110) cc_final: 0.4717 (ptt180) REVERT: J 173 GLN cc_start: 0.8708 (mt0) cc_final: 0.7822 (mp10) REVERT: J 205 LEU cc_start: 0.8881 (tp) cc_final: 0.8545 (tp) REVERT: J 234 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7706 (tttt) REVERT: J 279 TYR cc_start: 0.7920 (t80) cc_final: 0.7651 (t80) outliers start: 1 outliers final: 0 residues processed: 754 average time/residue: 0.1212 time to fit residues: 141.7987 Evaluate side-chains 637 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 199 optimal weight: 0.0060 chunk 192 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119391 restraints weight = 35360.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122799 restraints weight = 21020.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125178 restraints weight = 13943.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126790 restraints weight = 10086.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128183 restraints weight = 7866.534| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20040 Z= 0.152 Angle : 0.723 7.663 27260 Z= 0.358 Chirality : 0.041 0.169 3170 Planarity : 0.005 0.051 3350 Dihedral : 4.961 23.792 2690 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.74 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2480 helix: 0.87 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.68 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 144 TYR 0.035 0.002 TYR I 51 PHE 0.018 0.002 PHE A 64 TRP 0.015 0.001 TRP E 257 HIS 0.004 0.001 HIS I 245 Details of bonding type rmsd covalent geometry : bond 0.00334 (20010) covalent geometry : angle 0.72095 (27200) SS BOND : bond 0.00469 ( 30) SS BOND : angle 1.35840 ( 60) hydrogen bonds : bond 0.04190 ( 1311) hydrogen bonds : angle 4.43181 ( 3933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 755 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8897 (tp) cc_final: 0.8634 (tp) REVERT: A 73 ARG cc_start: 0.5820 (mmp-170) cc_final: 0.5136 (tpp80) REVERT: A 125 GLU cc_start: 0.7536 (tp30) cc_final: 0.7225 (tp30) REVERT: A 166 LEU cc_start: 0.8175 (tt) cc_final: 0.7640 (mt) REVERT: A 173 GLN cc_start: 0.8483 (mt0) cc_final: 0.7566 (mt0) REVERT: A 220 ILE cc_start: 0.8900 (tt) cc_final: 0.8612 (tt) REVERT: A 234 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7574 (ttpt) REVERT: A 235 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 32 ARG cc_start: 0.6550 (ttt-90) cc_final: 0.6058 (tpt170) REVERT: B 125 GLU cc_start: 0.7655 (tp30) cc_final: 0.7201 (tp30) REVERT: B 215 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 234 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7682 (ttpt) REVERT: B 278 LYS cc_start: 0.8316 (tttt) cc_final: 0.7731 (ttmt) REVERT: C 63 LEU cc_start: 0.8952 (tp) cc_final: 0.8692 (tp) REVERT: C 73 ARG cc_start: 0.6214 (mmp-170) cc_final: 0.5610 (tpp-160) REVERT: C 94 ARG cc_start: 0.5372 (ttm110) cc_final: 0.4687 (ptt180) REVERT: C 125 GLU cc_start: 0.7648 (tp30) cc_final: 0.7356 (tp30) REVERT: C 144 ARG cc_start: 0.8404 (ttp80) cc_final: 0.7902 (tmm-80) REVERT: C 173 GLN cc_start: 0.8804 (mt0) cc_final: 0.8398 (mt0) REVERT: C 177 LEU cc_start: 0.9025 (tp) cc_final: 0.8657 (tp) REVERT: C 220 ILE cc_start: 0.8557 (tt) cc_final: 0.8111 (tt) REVERT: C 234 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7643 (ttpt) REVERT: C 267 ASN cc_start: 0.8114 (t0) cc_final: 0.7719 (t0) REVERT: D 63 LEU cc_start: 0.8916 (tp) cc_final: 0.8679 (tp) REVERT: D 125 GLU cc_start: 0.7741 (tp30) cc_final: 0.7404 (tp30) REVERT: D 144 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8030 (tmm-80) REVERT: D 173 GLN cc_start: 0.8859 (mt0) cc_final: 0.7767 (mp10) REVERT: D 177 LEU cc_start: 0.9256 (tp) cc_final: 0.8999 (tp) REVERT: D 234 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7684 (tttt) REVERT: D 267 ASN cc_start: 0.8355 (t0) cc_final: 0.7714 (t0) REVERT: D 279 TYR cc_start: 0.8069 (t80) cc_final: 0.7764 (t80) REVERT: E 32 ARG cc_start: 0.7363 (ttt-90) cc_final: 0.6775 (tpp-160) REVERT: E 63 LEU cc_start: 0.8996 (tp) cc_final: 0.8775 (tp) REVERT: E 73 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7593 (tpp-160) REVERT: E 144 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8120 (ttp80) REVERT: E 166 LEU cc_start: 0.8217 (tt) cc_final: 0.7568 (mt) REVERT: E 173 GLN cc_start: 0.8690 (mt0) cc_final: 0.7836 (mp10) REVERT: E 217 GLU cc_start: 0.8363 (tt0) cc_final: 0.7983 (tt0) REVERT: E 231 GLU cc_start: 0.8307 (pp20) cc_final: 0.8001 (tm-30) REVERT: E 234 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7759 (tttt) REVERT: E 236 ASN cc_start: 0.7589 (m110) cc_final: 0.7315 (m110) REVERT: E 279 TYR cc_start: 0.8027 (t80) cc_final: 0.7661 (t80) REVERT: F 32 ARG cc_start: 0.6982 (ttt-90) cc_final: 0.6729 (ttt90) REVERT: F 63 LEU cc_start: 0.8860 (tp) cc_final: 0.8564 (tp) REVERT: F 125 GLU cc_start: 0.7730 (tp30) cc_final: 0.7380 (tp30) REVERT: F 166 LEU cc_start: 0.8138 (tt) cc_final: 0.7680 (mt) REVERT: F 173 GLN cc_start: 0.8464 (mt0) cc_final: 0.7602 (mt0) REVERT: F 219 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7298 (tm-30) REVERT: F 220 ILE cc_start: 0.8919 (tt) cc_final: 0.8637 (tt) REVERT: F 234 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7471 (ttpt) REVERT: F 235 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8359 (tm-30) REVERT: F 236 ASN cc_start: 0.7562 (m110) cc_final: 0.6877 (m110) REVERT: F 258 GLN cc_start: 0.8242 (tt0) cc_final: 0.8007 (tm-30) REVERT: G 32 ARG cc_start: 0.6828 (ttt-90) cc_final: 0.6244 (tpt170) REVERT: G 125 GLU cc_start: 0.7662 (tp30) cc_final: 0.7136 (tp30) REVERT: G 166 LEU cc_start: 0.8083 (tt) cc_final: 0.7426 (mt) REVERT: G 173 GLN cc_start: 0.8908 (mt0) cc_final: 0.7841 (mp10) REVERT: G 219 GLN cc_start: 0.7439 (tm-30) cc_final: 0.7165 (tm-30) REVERT: G 220 ILE cc_start: 0.8624 (tt) cc_final: 0.7900 (tt) REVERT: G 224 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7823 (ttpt) REVERT: G 234 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7523 (ttpt) REVERT: G 278 LYS cc_start: 0.8137 (tttt) cc_final: 0.7545 (ttmt) REVERT: H 32 ARG cc_start: 0.6397 (ttt-90) cc_final: 0.5739 (tpt170) REVERT: H 63 LEU cc_start: 0.8987 (tp) cc_final: 0.8728 (tp) REVERT: H 73 ARG cc_start: 0.6339 (mmp-170) cc_final: 0.5781 (tpp-160) REVERT: H 94 ARG cc_start: 0.5262 (ttm110) cc_final: 0.4590 (ptt180) REVERT: H 125 GLU cc_start: 0.7735 (tp30) cc_final: 0.7452 (tp30) REVERT: H 144 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8019 (tmm-80) REVERT: H 166 LEU cc_start: 0.8470 (tt) cc_final: 0.7842 (mt) REVERT: H 220 ILE cc_start: 0.8583 (tt) cc_final: 0.8228 (tt) REVERT: H 224 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7916 (ttpt) REVERT: H 231 GLU cc_start: 0.8143 (pp20) cc_final: 0.7918 (tm-30) REVERT: H 234 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7484 (ttpt) REVERT: H 267 ASN cc_start: 0.8283 (t0) cc_final: 0.7847 (t0) REVERT: I 32 ARG cc_start: 0.6852 (ttt-90) cc_final: 0.6428 (tpt170) REVERT: I 63 LEU cc_start: 0.8897 (tp) cc_final: 0.8696 (tp) REVERT: I 73 ARG cc_start: 0.5566 (mmp-170) cc_final: 0.4922 (tpt170) REVERT: I 125 GLU cc_start: 0.7771 (tp30) cc_final: 0.7456 (tp30) REVERT: I 166 LEU cc_start: 0.8183 (tt) cc_final: 0.7566 (mt) REVERT: I 173 GLN cc_start: 0.8878 (mt0) cc_final: 0.7996 (mt0) REVERT: I 192 PHE cc_start: 0.8458 (t80) cc_final: 0.8228 (t80) REVERT: I 208 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7960 (mtmt) REVERT: I 224 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8124 (ttpt) REVERT: I 231 GLU cc_start: 0.8335 (pp20) cc_final: 0.7852 (pp20) REVERT: I 234 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7649 (tttt) REVERT: I 267 ASN cc_start: 0.8410 (t0) cc_final: 0.7710 (t0) REVERT: I 279 TYR cc_start: 0.7946 (t80) cc_final: 0.7690 (t80) REVERT: J 32 ARG cc_start: 0.7262 (ttt-90) cc_final: 0.6700 (ttt90) REVERT: J 73 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7499 (tpp-160) REVERT: J 94 ARG cc_start: 0.5171 (ttm110) cc_final: 0.4707 (ptt180) REVERT: J 144 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8183 (tmm-80) REVERT: J 166 LEU cc_start: 0.8101 (tt) cc_final: 0.7365 (mt) REVERT: J 173 GLN cc_start: 0.8758 (mt0) cc_final: 0.7853 (mp10) REVERT: J 205 LEU cc_start: 0.8835 (tp) cc_final: 0.8599 (tp) REVERT: J 217 GLU cc_start: 0.8511 (tt0) cc_final: 0.8132 (tt0) REVERT: J 224 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8190 (ttpt) REVERT: J 234 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7711 (tttt) REVERT: J 235 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7999 (tm-30) REVERT: J 279 TYR cc_start: 0.8008 (t80) cc_final: 0.7655 (t80) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.1252 time to fit residues: 146.2243 Evaluate side-chains 640 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 203 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 156 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN J 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118503 restraints weight = 36382.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121698 restraints weight = 22245.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124022 restraints weight = 15235.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125566 restraints weight = 11369.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126761 restraints weight = 9126.409| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20040 Z= 0.152 Angle : 0.724 7.656 27260 Z= 0.358 Chirality : 0.041 0.181 3170 Planarity : 0.005 0.045 3350 Dihedral : 4.889 23.640 2690 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.15 % Favored : 91.81 % Rotamer: Outliers : 0.05 % Allowed : 1.59 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2480 helix: 0.93 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.70 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 144 TYR 0.025 0.002 TYR G 51 PHE 0.015 0.002 PHE D 134 TRP 0.018 0.002 TRP C 210 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00335 (20010) covalent geometry : angle 0.72195 (27200) SS BOND : bond 0.00760 ( 30) SS BOND : angle 1.42651 ( 60) hydrogen bonds : bond 0.04126 ( 1311) hydrogen bonds : angle 4.37473 ( 3933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 742 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8426 (t80) cc_final: 0.7891 (t80) REVERT: A 63 LEU cc_start: 0.8890 (tp) cc_final: 0.8630 (tp) REVERT: A 73 ARG cc_start: 0.5651 (mmp-170) cc_final: 0.5034 (tpt170) REVERT: A 125 GLU cc_start: 0.7527 (tp30) cc_final: 0.7261 (tp30) REVERT: A 166 LEU cc_start: 0.8097 (tt) cc_final: 0.7544 (mt) REVERT: A 173 GLN cc_start: 0.8438 (mt0) cc_final: 0.7569 (mt0) REVERT: A 234 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7464 (ttpt) REVERT: B 32 ARG cc_start: 0.6613 (ttt-90) cc_final: 0.6297 (tpt170) REVERT: B 125 GLU cc_start: 0.7687 (tp30) cc_final: 0.7281 (tp30) REVERT: B 215 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 234 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7664 (tttm) REVERT: B 278 LYS cc_start: 0.8169 (tttt) cc_final: 0.7920 (ttmt) REVERT: C 63 LEU cc_start: 0.8954 (tp) cc_final: 0.8688 (tp) REVERT: C 73 ARG cc_start: 0.5749 (mmp-170) cc_final: 0.5411 (tpp-160) REVERT: C 94 ARG cc_start: 0.5430 (ttm110) cc_final: 0.4712 (ptt180) REVERT: C 125 GLU cc_start: 0.7624 (tp30) cc_final: 0.7291 (tp30) REVERT: C 134 PHE cc_start: 0.8209 (t80) cc_final: 0.8003 (t80) REVERT: C 144 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7891 (tmm-80) REVERT: C 177 LEU cc_start: 0.9025 (tp) cc_final: 0.8692 (tp) REVERT: C 220 ILE cc_start: 0.8542 (tt) cc_final: 0.8080 (tt) REVERT: C 234 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7607 (ttpt) REVERT: C 278 LYS cc_start: 0.8138 (tttt) cc_final: 0.7795 (ttpt) REVERT: D 51 TYR cc_start: 0.8970 (t80) cc_final: 0.8643 (t80) REVERT: D 63 LEU cc_start: 0.8971 (tp) cc_final: 0.8737 (tp) REVERT: D 125 GLU cc_start: 0.7648 (tp30) cc_final: 0.7325 (tp30) REVERT: D 144 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8027 (tmm-80) REVERT: D 173 GLN cc_start: 0.8921 (mt0) cc_final: 0.8003 (mt0) REVERT: D 177 LEU cc_start: 0.9201 (tp) cc_final: 0.8927 (tp) REVERT: D 196 THR cc_start: 0.8553 (m) cc_final: 0.8350 (m) REVERT: D 234 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7699 (tttt) REVERT: D 267 ASN cc_start: 0.8456 (t0) cc_final: 0.7798 (t0) REVERT: E 32 ARG cc_start: 0.7315 (ttt-90) cc_final: 0.6748 (ttt90) REVERT: E 63 LEU cc_start: 0.9002 (tp) cc_final: 0.8800 (tp) REVERT: E 73 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7630 (tpp-160) REVERT: E 144 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8135 (ttp80) REVERT: E 166 LEU cc_start: 0.8152 (tt) cc_final: 0.7463 (mt) REVERT: E 173 GLN cc_start: 0.8712 (mt0) cc_final: 0.7798 (mp10) REVERT: E 231 GLU cc_start: 0.8368 (pp20) cc_final: 0.7894 (pp20) REVERT: E 234 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7818 (tttt) REVERT: E 256 GLU cc_start: 0.8544 (tt0) cc_final: 0.8237 (tt0) REVERT: E 279 TYR cc_start: 0.8027 (t80) cc_final: 0.7489 (t80) REVERT: F 32 ARG cc_start: 0.6993 (ttt-90) cc_final: 0.6726 (ttt90) REVERT: F 63 LEU cc_start: 0.8866 (tp) cc_final: 0.8562 (tp) REVERT: F 125 GLU cc_start: 0.7700 (tp30) cc_final: 0.7317 (tp30) REVERT: F 166 LEU cc_start: 0.8161 (tt) cc_final: 0.7657 (mt) REVERT: F 173 GLN cc_start: 0.8535 (mt0) cc_final: 0.7547 (mt0) REVERT: F 234 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7488 (ttpt) REVERT: F 256 GLU cc_start: 0.8223 (tt0) cc_final: 0.7742 (tt0) REVERT: F 258 GLN cc_start: 0.8254 (tt0) cc_final: 0.7996 (tm-30) REVERT: G 32 ARG cc_start: 0.6825 (ttt-90) cc_final: 0.6299 (tpt170) REVERT: G 51 TYR cc_start: 0.8559 (t80) cc_final: 0.8179 (t80) REVERT: G 125 GLU cc_start: 0.7552 (tp30) cc_final: 0.6918 (tp30) REVERT: G 166 LEU cc_start: 0.8090 (tt) cc_final: 0.7456 (mt) REVERT: G 173 GLN cc_start: 0.8925 (mt0) cc_final: 0.7835 (mp10) REVERT: G 220 ILE cc_start: 0.8632 (tt) cc_final: 0.8296 (tt) REVERT: G 224 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7752 (ttpt) REVERT: G 234 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7410 (ttpt) REVERT: G 274 SER cc_start: 0.7716 (p) cc_final: 0.7373 (p) REVERT: G 278 LYS cc_start: 0.8064 (tttt) cc_final: 0.7752 (ttmt) REVERT: H 32 ARG cc_start: 0.6605 (ttt-90) cc_final: 0.5746 (tpt170) REVERT: H 63 LEU cc_start: 0.8980 (tp) cc_final: 0.8732 (tp) REVERT: H 73 ARG cc_start: 0.6008 (mmp-170) cc_final: 0.5403 (tpp-160) REVERT: H 94 ARG cc_start: 0.5283 (ttm110) cc_final: 0.4591 (ptt180) REVERT: H 125 GLU cc_start: 0.7625 (tp30) cc_final: 0.7272 (tp30) REVERT: H 144 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8028 (tmm-80) REVERT: H 166 LEU cc_start: 0.8528 (tt) cc_final: 0.7920 (mt) REVERT: H 220 ILE cc_start: 0.8608 (tt) cc_final: 0.8297 (tt) REVERT: H 234 LYS cc_start: 0.8397 (ttmt) cc_final: 0.7477 (ttpt) REVERT: H 267 ASN cc_start: 0.8139 (t0) cc_final: 0.7746 (t0) REVERT: I 32 ARG cc_start: 0.6901 (ttt-90) cc_final: 0.6452 (tpt170) REVERT: I 51 TYR cc_start: 0.9092 (t80) cc_final: 0.8769 (t80) REVERT: I 63 LEU cc_start: 0.8899 (tp) cc_final: 0.8697 (tp) REVERT: I 73 ARG cc_start: 0.5558 (mmp-170) cc_final: 0.4650 (tpt170) REVERT: I 125 GLU cc_start: 0.7594 (tp30) cc_final: 0.7256 (tp30) REVERT: I 144 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8082 (tmm-80) REVERT: I 166 LEU cc_start: 0.8175 (tt) cc_final: 0.7535 (mt) REVERT: I 173 GLN cc_start: 0.8986 (mt0) cc_final: 0.8150 (mt0) REVERT: I 192 PHE cc_start: 0.8471 (t80) cc_final: 0.8269 (t80) REVERT: I 208 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7997 (mtmt) REVERT: I 224 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8325 (ttpt) REVERT: I 231 GLU cc_start: 0.8248 (pp20) cc_final: 0.7792 (pp20) REVERT: I 234 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7533 (tttt) REVERT: I 267 ASN cc_start: 0.8325 (t0) cc_final: 0.7661 (t0) REVERT: I 279 TYR cc_start: 0.8012 (t80) cc_final: 0.7683 (t80) REVERT: J 32 ARG cc_start: 0.7143 (ttt-90) cc_final: 0.6575 (ttt90) REVERT: J 55 PHE cc_start: 0.8973 (m-80) cc_final: 0.8765 (m-10) REVERT: J 63 LEU cc_start: 0.9035 (tp) cc_final: 0.8804 (tp) REVERT: J 73 ARG cc_start: 0.7850 (ttp-110) cc_final: 0.7516 (tpp-160) REVERT: J 144 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8207 (tmm-80) REVERT: J 166 LEU cc_start: 0.8184 (tt) cc_final: 0.7475 (mt) REVERT: J 173 GLN cc_start: 0.8757 (mt0) cc_final: 0.7828 (mp10) REVERT: J 197 ARG cc_start: 0.8586 (mtt90) cc_final: 0.8235 (mtt90) REVERT: J 210 TRP cc_start: 0.8637 (t60) cc_final: 0.8366 (t60) REVERT: J 217 GLU cc_start: 0.8534 (tt0) cc_final: 0.7928 (tt0) REVERT: J 224 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8237 (ttpt) REVERT: J 234 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7774 (tttt) REVERT: J 256 GLU cc_start: 0.8486 (tt0) cc_final: 0.8207 (tt0) REVERT: J 279 TYR cc_start: 0.8084 (t80) cc_final: 0.7525 (t80) outliers start: 1 outliers final: 0 residues processed: 743 average time/residue: 0.1311 time to fit residues: 150.7317 Evaluate side-chains 624 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 38 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN C 175 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN J 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120132 restraints weight = 36121.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123388 restraints weight = 21982.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125721 restraints weight = 15029.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127282 restraints weight = 11158.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128626 restraints weight = 8905.740| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20040 Z= 0.143 Angle : 0.734 10.555 27260 Z= 0.357 Chirality : 0.041 0.284 3170 Planarity : 0.005 0.044 3350 Dihedral : 4.830 23.495 2690 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.42 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2480 helix: 0.92 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -3.75 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 144 TYR 0.038 0.002 TYR A 51 PHE 0.020 0.002 PHE H 55 TRP 0.029 0.002 TRP A 257 HIS 0.007 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00314 (20010) covalent geometry : angle 0.73132 (27200) SS BOND : bond 0.00276 ( 30) SS BOND : angle 1.53879 ( 60) hydrogen bonds : bond 0.04008 ( 1311) hydrogen bonds : angle 4.33426 ( 3933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8894 (tp) cc_final: 0.8681 (tp) REVERT: A 73 ARG cc_start: 0.5591 (mmp-170) cc_final: 0.4993 (tpt170) REVERT: A 125 GLU cc_start: 0.7462 (tp30) cc_final: 0.7200 (tp30) REVERT: A 166 LEU cc_start: 0.8051 (tt) cc_final: 0.7451 (mt) REVERT: A 173 GLN cc_start: 0.8414 (mt0) cc_final: 0.7508 (mt0) REVERT: A 210 TRP cc_start: 0.8772 (t60) cc_final: 0.8464 (t60) REVERT: A 234 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7576 (ttpt) REVERT: A 256 GLU cc_start: 0.8453 (tt0) cc_final: 0.7983 (tt0) REVERT: A 279 TYR cc_start: 0.7098 (t80) cc_final: 0.6196 (t80) REVERT: B 32 ARG cc_start: 0.6612 (ttt-90) cc_final: 0.6296 (tpt170) REVERT: B 125 GLU cc_start: 0.7570 (tp30) cc_final: 0.7122 (tp30) REVERT: B 215 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 234 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7680 (tttm) REVERT: B 256 GLU cc_start: 0.8547 (tt0) cc_final: 0.8344 (tt0) REVERT: B 278 LYS cc_start: 0.8066 (tttt) cc_final: 0.7833 (tttt) REVERT: B 279 TYR cc_start: 0.7733 (t80) cc_final: 0.7284 (t80) REVERT: C 63 LEU cc_start: 0.8937 (tp) cc_final: 0.8669 (tp) REVERT: C 73 ARG cc_start: 0.5756 (mmp-170) cc_final: 0.5396 (tpp-160) REVERT: C 94 ARG cc_start: 0.5332 (ttm110) cc_final: 0.4613 (ptt180) REVERT: C 125 GLU cc_start: 0.7576 (tp30) cc_final: 0.7259 (tp30) REVERT: C 144 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7875 (tmm-80) REVERT: C 177 LEU cc_start: 0.9000 (tp) cc_final: 0.8662 (tp) REVERT: C 220 ILE cc_start: 0.8523 (tt) cc_final: 0.8089 (tt) REVERT: C 234 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7566 (ttpt) REVERT: C 278 LYS cc_start: 0.8099 (tttt) cc_final: 0.7689 (ttpt) REVERT: D 51 TYR cc_start: 0.8943 (t80) cc_final: 0.8636 (t80) REVERT: D 63 LEU cc_start: 0.8973 (tp) cc_final: 0.8724 (tp) REVERT: D 125 GLU cc_start: 0.7510 (tp30) cc_final: 0.7195 (tp30) REVERT: D 134 PHE cc_start: 0.8026 (t80) cc_final: 0.7786 (t80) REVERT: D 144 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8021 (tmm-80) REVERT: D 173 GLN cc_start: 0.8939 (mt0) cc_final: 0.7974 (mt0) REVERT: D 177 LEU cc_start: 0.9187 (tp) cc_final: 0.8934 (tp) REVERT: D 234 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7624 (tttt) REVERT: D 267 ASN cc_start: 0.8316 (t0) cc_final: 0.7617 (t0) REVERT: E 32 ARG cc_start: 0.7314 (ttt-90) cc_final: 0.6741 (ttt90) REVERT: E 63 LEU cc_start: 0.9018 (tp) cc_final: 0.8784 (tp) REVERT: E 73 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7617 (tpp-160) REVERT: E 144 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8107 (ttp80) REVERT: E 166 LEU cc_start: 0.8114 (tt) cc_final: 0.7411 (mt) REVERT: E 173 GLN cc_start: 0.8676 (mt0) cc_final: 0.7721 (mp10) REVERT: E 217 GLU cc_start: 0.7989 (tt0) cc_final: 0.7642 (tt0) REVERT: E 234 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7736 (tttt) REVERT: E 235 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8009 (tm-30) REVERT: E 256 GLU cc_start: 0.8529 (tt0) cc_final: 0.8122 (tt0) REVERT: E 279 TYR cc_start: 0.8105 (t80) cc_final: 0.7525 (t80) REVERT: F 32 ARG cc_start: 0.6998 (ttt-90) cc_final: 0.6733 (ttt90) REVERT: F 63 LEU cc_start: 0.8893 (tp) cc_final: 0.8590 (tp) REVERT: F 125 GLU cc_start: 0.7659 (tp30) cc_final: 0.7280 (tp30) REVERT: F 166 LEU cc_start: 0.8084 (tt) cc_final: 0.7623 (mt) REVERT: F 173 GLN cc_start: 0.8521 (mt0) cc_final: 0.7517 (mt0) REVERT: F 206 GLN cc_start: 0.8809 (tt0) cc_final: 0.7926 (tp40) REVERT: F 210 TRP cc_start: 0.8774 (t60) cc_final: 0.8490 (t60) REVERT: F 234 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7492 (ttpt) REVERT: F 258 GLN cc_start: 0.8158 (tt0) cc_final: 0.7823 (tm-30) REVERT: G 32 ARG cc_start: 0.6769 (ttt-90) cc_final: 0.6293 (tpt170) REVERT: G 51 TYR cc_start: 0.8482 (t80) cc_final: 0.8137 (t80) REVERT: G 125 GLU cc_start: 0.7508 (tp30) cc_final: 0.6861 (tp30) REVERT: G 166 LEU cc_start: 0.8096 (tt) cc_final: 0.7448 (mt) REVERT: G 173 GLN cc_start: 0.8931 (mt0) cc_final: 0.7833 (mp10) REVERT: G 220 ILE cc_start: 0.8626 (tt) cc_final: 0.8378 (tt) REVERT: G 224 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7713 (ttpt) REVERT: G 226 THR cc_start: 0.8403 (m) cc_final: 0.8088 (p) REVERT: G 234 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7456 (ttpt) REVERT: G 274 SER cc_start: 0.7688 (p) cc_final: 0.7215 (p) REVERT: G 279 TYR cc_start: 0.7704 (t80) cc_final: 0.7276 (t80) REVERT: H 32 ARG cc_start: 0.6614 (ttt-90) cc_final: 0.5807 (tpt170) REVERT: H 63 LEU cc_start: 0.8961 (tp) cc_final: 0.8716 (tp) REVERT: H 73 ARG cc_start: 0.5603 (mmp-170) cc_final: 0.5275 (tpp-160) REVERT: H 94 ARG cc_start: 0.5189 (ttm110) cc_final: 0.4522 (ptt180) REVERT: H 125 GLU cc_start: 0.7582 (tp30) cc_final: 0.7296 (tp30) REVERT: H 166 LEU cc_start: 0.8479 (tt) cc_final: 0.7875 (mt) REVERT: H 231 GLU cc_start: 0.8126 (pp20) cc_final: 0.7789 (tm-30) REVERT: H 234 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7453 (ttpt) REVERT: I 32 ARG cc_start: 0.6871 (ttt-90) cc_final: 0.6446 (tpt170) REVERT: I 51 TYR cc_start: 0.9061 (t80) cc_final: 0.8715 (t80) REVERT: I 73 ARG cc_start: 0.5512 (mmp-170) cc_final: 0.4656 (tpt170) REVERT: I 125 GLU cc_start: 0.7503 (tp30) cc_final: 0.7211 (tp30) REVERT: I 144 ARG cc_start: 0.8500 (ttp80) cc_final: 0.7954 (tmm-80) REVERT: I 173 GLN cc_start: 0.8906 (mt0) cc_final: 0.8083 (mt0) REVERT: I 192 PHE cc_start: 0.8445 (t80) cc_final: 0.8237 (t80) REVERT: I 208 LYS cc_start: 0.8310 (mtpp) cc_final: 0.8001 (mtmt) REVERT: I 224 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8164 (ttpt) REVERT: I 231 GLU cc_start: 0.8236 (pp20) cc_final: 0.7767 (pp20) REVERT: I 234 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7523 (tttt) REVERT: I 267 ASN cc_start: 0.8325 (t0) cc_final: 0.7687 (t0) REVERT: I 279 TYR cc_start: 0.7886 (t80) cc_final: 0.7660 (t80) REVERT: J 32 ARG cc_start: 0.7138 (ttt-90) cc_final: 0.6594 (ttt90) REVERT: J 55 PHE cc_start: 0.8906 (m-80) cc_final: 0.8602 (m-10) REVERT: J 63 LEU cc_start: 0.8989 (tp) cc_final: 0.8789 (tp) REVERT: J 73 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7595 (tpp-160) REVERT: J 144 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8104 (tmm-80) REVERT: J 166 LEU cc_start: 0.8043 (tt) cc_final: 0.7278 (mt) REVERT: J 173 GLN cc_start: 0.8742 (mt0) cc_final: 0.7812 (mp10) REVERT: J 210 TRP cc_start: 0.8591 (t60) cc_final: 0.8349 (t60) REVERT: J 217 GLU cc_start: 0.8509 (tt0) cc_final: 0.8117 (tt0) REVERT: J 224 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8230 (ttpt) REVERT: J 234 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7761 (tttt) REVERT: J 235 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7959 (tm-30) REVERT: J 256 GLU cc_start: 0.8469 (tt0) cc_final: 0.8071 (tt0) REVERT: J 279 TYR cc_start: 0.8001 (t80) cc_final: 0.7451 (t80) outliers start: 0 outliers final: 0 residues processed: 745 average time/residue: 0.1246 time to fit residues: 143.9837 Evaluate side-chains 623 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 141 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 230 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122454 restraints weight = 35182.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125813 restraints weight = 21455.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128099 restraints weight = 14624.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129968 restraints weight = 10893.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131216 restraints weight = 8567.639| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20040 Z= 0.134 Angle : 0.730 10.200 27260 Z= 0.349 Chirality : 0.041 0.286 3170 Planarity : 0.005 0.047 3350 Dihedral : 4.723 23.626 2690 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 0.05 % Allowed : 0.87 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2480 helix: 0.99 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -3.75 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 144 TYR 0.031 0.002 TYR F 279 PHE 0.019 0.002 PHE F 134 TRP 0.029 0.001 TRP E 210 HIS 0.005 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00285 (20010) covalent geometry : angle 0.72745 (27200) SS BOND : bond 0.00235 ( 30) SS BOND : angle 1.45097 ( 60) hydrogen bonds : bond 0.03806 ( 1311) hydrogen bonds : angle 4.24196 ( 3933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 761 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8930 (tp) cc_final: 0.8709 (tp) REVERT: A 73 ARG cc_start: 0.5571 (mmp-170) cc_final: 0.5032 (tpt170) REVERT: A 125 GLU cc_start: 0.7484 (tp30) cc_final: 0.7170 (tp30) REVERT: A 166 LEU cc_start: 0.7929 (tt) cc_final: 0.7310 (mt) REVERT: A 173 GLN cc_start: 0.8383 (mt0) cc_final: 0.7463 (mt0) REVERT: A 210 TRP cc_start: 0.8910 (t60) cc_final: 0.8504 (t60) REVERT: A 234 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7458 (ttpt) REVERT: A 256 GLU cc_start: 0.8459 (tt0) cc_final: 0.8013 (tt0) REVERT: A 279 TYR cc_start: 0.7580 (t80) cc_final: 0.6824 (t80) REVERT: B 32 ARG cc_start: 0.6631 (ttt-90) cc_final: 0.6284 (tpt170) REVERT: B 125 GLU cc_start: 0.7569 (tp30) cc_final: 0.7112 (tp30) REVERT: B 215 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 234 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7501 (ttpt) REVERT: B 256 GLU cc_start: 0.8538 (tt0) cc_final: 0.8278 (tt0) REVERT: B 279 TYR cc_start: 0.7816 (t80) cc_final: 0.7380 (t80) REVERT: C 63 LEU cc_start: 0.8871 (tp) cc_final: 0.8595 (tp) REVERT: C 94 ARG cc_start: 0.5300 (ttm110) cc_final: 0.4586 (ptt180) REVERT: C 125 GLU cc_start: 0.7605 (tp30) cc_final: 0.7258 (tp30) REVERT: C 144 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7961 (tmm-80) REVERT: C 177 LEU cc_start: 0.9023 (tp) cc_final: 0.8664 (tp) REVERT: C 220 ILE cc_start: 0.8550 (tt) cc_final: 0.8098 (tt) REVERT: C 234 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7482 (ttpt) REVERT: D 51 TYR cc_start: 0.8874 (t80) cc_final: 0.8515 (t80) REVERT: D 123 PHE cc_start: 0.9083 (m-10) cc_final: 0.8882 (m-80) REVERT: D 125 GLU cc_start: 0.7539 (tp30) cc_final: 0.7154 (tp30) REVERT: D 134 PHE cc_start: 0.8119 (t80) cc_final: 0.7905 (t80) REVERT: D 144 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7986 (tmm-80) REVERT: D 173 GLN cc_start: 0.8929 (mt0) cc_final: 0.7960 (mt0) REVERT: D 177 LEU cc_start: 0.9162 (tp) cc_final: 0.8914 (tp) REVERT: D 196 THR cc_start: 0.8399 (m) cc_final: 0.8195 (m) REVERT: D 234 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7668 (tttt) REVERT: D 267 ASN cc_start: 0.8312 (t0) cc_final: 0.7664 (t0) REVERT: E 32 ARG cc_start: 0.7260 (ttt-90) cc_final: 0.6711 (ttt90) REVERT: E 55 PHE cc_start: 0.8801 (m-80) cc_final: 0.8596 (m-10) REVERT: E 63 LEU cc_start: 0.8992 (tp) cc_final: 0.8760 (tp) REVERT: E 73 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7616 (tpp-160) REVERT: E 144 ARG cc_start: 0.8337 (ttp80) cc_final: 0.8104 (ttp80) REVERT: E 166 LEU cc_start: 0.8098 (tt) cc_final: 0.7464 (mt) REVERT: E 173 GLN cc_start: 0.8686 (mt0) cc_final: 0.7911 (mp10) REVERT: E 234 LYS cc_start: 0.8368 (ttmt) cc_final: 0.7742 (tttt) REVERT: E 235 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8049 (tm-30) REVERT: E 256 GLU cc_start: 0.8533 (tt0) cc_final: 0.8075 (tt0) REVERT: E 279 TYR cc_start: 0.8162 (t80) cc_final: 0.7538 (t80) REVERT: F 32 ARG cc_start: 0.6925 (ttt-90) cc_final: 0.6692 (ttt90) REVERT: F 63 LEU cc_start: 0.8892 (tp) cc_final: 0.8646 (tp) REVERT: F 166 LEU cc_start: 0.8049 (tt) cc_final: 0.7580 (mt) REVERT: F 173 GLN cc_start: 0.8545 (mt0) cc_final: 0.7606 (mt0) REVERT: F 210 TRP cc_start: 0.8714 (t60) cc_final: 0.8489 (t60) REVERT: F 234 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7488 (ttpt) REVERT: F 256 GLU cc_start: 0.8389 (tt0) cc_final: 0.7878 (tt0) REVERT: G 32 ARG cc_start: 0.6850 (ttt-90) cc_final: 0.6291 (tpt170) REVERT: G 51 TYR cc_start: 0.8443 (t80) cc_final: 0.8098 (t80) REVERT: G 166 LEU cc_start: 0.8051 (tt) cc_final: 0.7384 (mt) REVERT: G 173 GLN cc_start: 0.8892 (mt0) cc_final: 0.7785 (mp10) REVERT: G 220 ILE cc_start: 0.8597 (tt) cc_final: 0.8188 (tt) REVERT: G 224 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7811 (ttpt) REVERT: G 226 THR cc_start: 0.8357 (m) cc_final: 0.8061 (p) REVERT: G 234 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7529 (ttpt) REVERT: G 256 GLU cc_start: 0.8546 (tt0) cc_final: 0.8335 (tt0) REVERT: G 274 SER cc_start: 0.7754 (p) cc_final: 0.7303 (p) REVERT: G 279 TYR cc_start: 0.7878 (t80) cc_final: 0.7380 (t80) REVERT: H 32 ARG cc_start: 0.6887 (ttt-90) cc_final: 0.5759 (tpt170) REVERT: H 63 LEU cc_start: 0.8911 (tp) cc_final: 0.8631 (tp) REVERT: H 73 ARG cc_start: 0.5761 (mmp-170) cc_final: 0.5410 (tpp-160) REVERT: H 94 ARG cc_start: 0.5199 (ttm110) cc_final: 0.4458 (ptt180) REVERT: H 125 GLU cc_start: 0.7582 (tp30) cc_final: 0.7363 (tp30) REVERT: H 144 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7950 (tmm-80) REVERT: H 220 ILE cc_start: 0.8624 (tt) cc_final: 0.8317 (tt) REVERT: H 231 GLU cc_start: 0.8008 (pp20) cc_final: 0.7651 (tm-30) REVERT: H 234 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7286 (ttpt) REVERT: I 63 LEU cc_start: 0.8939 (tp) cc_final: 0.8712 (tp) REVERT: I 73 ARG cc_start: 0.5517 (mmp-170) cc_final: 0.4826 (tpt170) REVERT: I 123 PHE cc_start: 0.9142 (m-10) cc_final: 0.8356 (m-80) REVERT: I 125 GLU cc_start: 0.7533 (tp30) cc_final: 0.7128 (tp30) REVERT: I 144 ARG cc_start: 0.8467 (ttp80) cc_final: 0.7927 (tmm-80) REVERT: I 166 LEU cc_start: 0.8101 (tt) cc_final: 0.7414 (mt) REVERT: I 173 GLN cc_start: 0.8906 (mt0) cc_final: 0.8061 (mt0) REVERT: I 208 LYS cc_start: 0.8328 (mtpp) cc_final: 0.8004 (mtmt) REVERT: I 224 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8098 (ttpt) REVERT: I 234 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7730 (tttt) REVERT: I 258 GLN cc_start: 0.8189 (tt0) cc_final: 0.7835 (tm-30) REVERT: I 267 ASN cc_start: 0.8239 (t0) cc_final: 0.7490 (t0) REVERT: I 274 SER cc_start: 0.8001 (p) cc_final: 0.6873 (p) REVERT: J 32 ARG cc_start: 0.7113 (ttt-90) cc_final: 0.6584 (ttt90) REVERT: J 55 PHE cc_start: 0.8872 (m-80) cc_final: 0.8640 (m-10) REVERT: J 73 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7589 (tpp-160) REVERT: J 118 LEU cc_start: 0.8662 (tp) cc_final: 0.8444 (tp) REVERT: J 144 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8072 (tmm-80) REVERT: J 166 LEU cc_start: 0.8010 (tt) cc_final: 0.7288 (mt) REVERT: J 173 GLN cc_start: 0.8568 (mt0) cc_final: 0.7686 (mp10) REVERT: J 217 GLU cc_start: 0.8509 (tt0) cc_final: 0.8186 (tt0) REVERT: J 234 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7723 (tttt) REVERT: J 256 GLU cc_start: 0.8542 (tt0) cc_final: 0.8134 (tt0) REVERT: J 279 TYR cc_start: 0.8123 (t80) cc_final: 0.7544 (t80) outliers start: 1 outliers final: 0 residues processed: 762 average time/residue: 0.1265 time to fit residues: 149.2277 Evaluate side-chains 644 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 644 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 230 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 111 optimal weight: 20.0000 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 175 GLN C 175 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN G 48 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123782 restraints weight = 35657.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127094 restraints weight = 21873.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129493 restraints weight = 14966.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131201 restraints weight = 11091.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132355 restraints weight = 8747.827| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20040 Z= 0.135 Angle : 0.741 9.598 27260 Z= 0.356 Chirality : 0.040 0.292 3170 Planarity : 0.005 0.050 3350 Dihedral : 4.689 24.355 2690 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2480 helix: 1.01 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -3.65 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 144 TYR 0.030 0.002 TYR I 51 PHE 0.016 0.001 PHE C 134 TRP 0.030 0.002 TRP J 210 HIS 0.008 0.001 HIS H 245 Details of bonding type rmsd covalent geometry : bond 0.00290 (20010) covalent geometry : angle 0.73756 (27200) SS BOND : bond 0.00255 ( 30) SS BOND : angle 1.77120 ( 60) hydrogen bonds : bond 0.03723 ( 1311) hydrogen bonds : angle 4.22178 ( 3933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 758 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.5523 (mmp-170) cc_final: 0.4997 (tpt170) REVERT: A 125 GLU cc_start: 0.7439 (tp30) cc_final: 0.7169 (tp30) REVERT: A 166 LEU cc_start: 0.7844 (tt) cc_final: 0.7299 (mt) REVERT: A 173 GLN cc_start: 0.8415 (mt0) cc_final: 0.7484 (mt0) REVERT: A 210 TRP cc_start: 0.8697 (t60) cc_final: 0.8472 (t60) REVERT: A 217 GLU cc_start: 0.8776 (tt0) cc_final: 0.8457 (tt0) REVERT: A 234 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7517 (ttpt) REVERT: A 274 SER cc_start: 0.8240 (p) cc_final: 0.7369 (p) REVERT: B 32 ARG cc_start: 0.6716 (ttt-90) cc_final: 0.6328 (tpt170) REVERT: B 125 GLU cc_start: 0.7548 (tp30) cc_final: 0.7109 (tp30) REVERT: B 234 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7538 (tttm) REVERT: B 256 GLU cc_start: 0.8675 (tt0) cc_final: 0.8386 (tt0) REVERT: B 274 SER cc_start: 0.7771 (p) cc_final: 0.7374 (p) REVERT: B 278 LYS cc_start: 0.7813 (tttt) cc_final: 0.7443 (ttpt) REVERT: B 279 TYR cc_start: 0.7925 (t80) cc_final: 0.7401 (t80) REVERT: C 63 LEU cc_start: 0.8865 (tp) cc_final: 0.8565 (tp) REVERT: C 73 ARG cc_start: 0.5073 (mpt180) cc_final: 0.4263 (tpt170) REVERT: C 94 ARG cc_start: 0.5343 (ttm110) cc_final: 0.4642 (ptt180) REVERT: C 125 GLU cc_start: 0.7661 (tp30) cc_final: 0.7317 (tp30) REVERT: C 144 ARG cc_start: 0.8422 (ttp80) cc_final: 0.7967 (tmm-80) REVERT: C 177 LEU cc_start: 0.9010 (tp) cc_final: 0.8665 (tp) REVERT: C 220 ILE cc_start: 0.8474 (tt) cc_final: 0.8050 (tt) REVERT: C 231 GLU cc_start: 0.8063 (pp20) cc_final: 0.7779 (tm-30) REVERT: C 234 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7445 (ttpt) REVERT: D 51 TYR cc_start: 0.8859 (t80) cc_final: 0.8500 (t80) REVERT: D 63 LEU cc_start: 0.8971 (tp) cc_final: 0.8740 (tp) REVERT: D 123 PHE cc_start: 0.9094 (m-10) cc_final: 0.8879 (m-80) REVERT: D 173 GLN cc_start: 0.8943 (mt0) cc_final: 0.8010 (mt0) REVERT: D 177 LEU cc_start: 0.9191 (tp) cc_final: 0.8925 (tp) REVERT: D 217 GLU cc_start: 0.8641 (tt0) cc_final: 0.8317 (tt0) REVERT: D 234 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7643 (tttt) REVERT: D 258 GLN cc_start: 0.8172 (tt0) cc_final: 0.7776 (tm-30) REVERT: D 267 ASN cc_start: 0.8242 (t0) cc_final: 0.7585 (t0) REVERT: E 32 ARG cc_start: 0.7123 (ttt-90) cc_final: 0.6729 (ttt90) REVERT: E 55 PHE cc_start: 0.8813 (m-80) cc_final: 0.8430 (m-10) REVERT: E 63 LEU cc_start: 0.9003 (tp) cc_final: 0.8767 (tp) REVERT: E 73 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7570 (tpp-160) REVERT: E 118 LEU cc_start: 0.8697 (tp) cc_final: 0.8495 (tp) REVERT: E 144 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8092 (ttp80) REVERT: E 166 LEU cc_start: 0.8109 (tt) cc_final: 0.7496 (mt) REVERT: E 173 GLN cc_start: 0.8689 (mt0) cc_final: 0.7926 (mp10) REVERT: E 234 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7791 (tttt) REVERT: E 235 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8101 (tm-30) REVERT: E 256 GLU cc_start: 0.8515 (tt0) cc_final: 0.7982 (tt0) REVERT: E 279 TYR cc_start: 0.8221 (t80) cc_final: 0.7687 (t80) REVERT: F 32 ARG cc_start: 0.6874 (ttt-90) cc_final: 0.6674 (ttt90) REVERT: F 63 LEU cc_start: 0.8854 (tp) cc_final: 0.8640 (tp) REVERT: F 166 LEU cc_start: 0.7884 (tt) cc_final: 0.7340 (mt) REVERT: F 173 GLN cc_start: 0.8558 (mt0) cc_final: 0.7606 (mt0) REVERT: F 206 GLN cc_start: 0.8901 (tt0) cc_final: 0.7912 (tm-30) REVERT: F 210 TRP cc_start: 0.8752 (t60) cc_final: 0.8514 (t60) REVERT: F 217 GLU cc_start: 0.8721 (tt0) cc_final: 0.8376 (tt0) REVERT: F 234 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7462 (ttpt) REVERT: F 256 GLU cc_start: 0.8347 (tt0) cc_final: 0.7907 (tt0) REVERT: F 274 SER cc_start: 0.8065 (p) cc_final: 0.6911 (p) REVERT: G 32 ARG cc_start: 0.6871 (ttt-90) cc_final: 0.6291 (tpt170) REVERT: G 166 LEU cc_start: 0.8048 (tt) cc_final: 0.7376 (mt) REVERT: G 173 GLN cc_start: 0.8905 (mt0) cc_final: 0.7760 (mp10) REVERT: G 224 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7810 (ttpt) REVERT: G 226 THR cc_start: 0.8390 (m) cc_final: 0.8065 (p) REVERT: G 234 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7434 (ttpt) REVERT: G 236 ASN cc_start: 0.7336 (m110) cc_final: 0.6681 (m-40) REVERT: G 256 GLU cc_start: 0.8673 (tt0) cc_final: 0.8463 (tt0) REVERT: G 274 SER cc_start: 0.7733 (p) cc_final: 0.6754 (p) REVERT: G 278 LYS cc_start: 0.7691 (tttt) cc_final: 0.7307 (ttmt) REVERT: G 279 TYR cc_start: 0.7898 (t80) cc_final: 0.7397 (t80) REVERT: H 32 ARG cc_start: 0.6907 (ttt-90) cc_final: 0.5777 (tpt170) REVERT: H 63 LEU cc_start: 0.8894 (tp) cc_final: 0.8626 (tp) REVERT: H 73 ARG cc_start: 0.5843 (mmp-170) cc_final: 0.5341 (tpt170) REVERT: H 94 ARG cc_start: 0.5210 (ttm110) cc_final: 0.4487 (ptt180) REVERT: H 125 GLU cc_start: 0.7688 (tp30) cc_final: 0.7288 (tp30) REVERT: H 144 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7992 (tmm-80) REVERT: H 166 LEU cc_start: 0.8464 (tt) cc_final: 0.7870 (mt) REVERT: H 220 ILE cc_start: 0.8595 (tt) cc_final: 0.8256 (tt) REVERT: H 234 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7272 (ttpt) REVERT: I 51 TYR cc_start: 0.9045 (t80) cc_final: 0.8666 (t80) REVERT: I 63 LEU cc_start: 0.8947 (tp) cc_final: 0.8731 (tp) REVERT: I 73 ARG cc_start: 0.5503 (mmp-170) cc_final: 0.4836 (tpt170) REVERT: I 123 PHE cc_start: 0.9128 (m-10) cc_final: 0.8860 (m-80) REVERT: I 125 GLU cc_start: 0.7511 (tp30) cc_final: 0.7180 (tp30) REVERT: I 144 ARG cc_start: 0.8449 (ttp80) cc_final: 0.7897 (tmm-80) REVERT: I 173 GLN cc_start: 0.8913 (mt0) cc_final: 0.8050 (mt0) REVERT: I 208 LYS cc_start: 0.8315 (mtpp) cc_final: 0.8008 (mtmt) REVERT: I 224 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8136 (ttpt) REVERT: I 234 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7719 (tttt) REVERT: I 258 GLN cc_start: 0.8219 (tt0) cc_final: 0.7844 (tm-30) REVERT: I 274 SER cc_start: 0.7983 (p) cc_final: 0.6859 (p) REVERT: J 32 ARG cc_start: 0.6966 (ttt-90) cc_final: 0.6569 (ttt90) REVERT: J 55 PHE cc_start: 0.8863 (m-80) cc_final: 0.8607 (m-10) REVERT: J 73 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7590 (tpp-160) REVERT: J 118 LEU cc_start: 0.8641 (tp) cc_final: 0.8424 (tp) REVERT: J 144 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8024 (tmm-80) REVERT: J 166 LEU cc_start: 0.8165 (tt) cc_final: 0.7461 (mt) REVERT: J 173 GLN cc_start: 0.8593 (mt0) cc_final: 0.7705 (mp10) REVERT: J 234 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7741 (tttt) REVERT: J 235 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7753 (tm-30) REVERT: J 236 ASN cc_start: 0.7472 (m-40) cc_final: 0.6997 (m110) REVERT: J 256 GLU cc_start: 0.8523 (tt0) cc_final: 0.8093 (tt0) REVERT: J 274 SER cc_start: 0.7790 (p) cc_final: 0.7165 (p) REVERT: J 279 TYR cc_start: 0.8207 (t80) cc_final: 0.7680 (t80) outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 0.1310 time to fit residues: 155.0739 Evaluate side-chains 636 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 175 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 103 optimal weight: 0.0170 chunk 244 optimal weight: 0.9990 chunk 198 optimal weight: 0.0370 chunk 121 optimal weight: 0.2980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 175 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN H 175 GLN H 236 ASN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124498 restraints weight = 35573.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127861 restraints weight = 21720.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130295 restraints weight = 14825.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.131973 restraints weight = 10968.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133345 restraints weight = 8708.834| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20040 Z= 0.134 Angle : 0.741 9.883 27260 Z= 0.353 Chirality : 0.040 0.250 3170 Planarity : 0.005 0.049 3350 Dihedral : 4.610 23.294 2690 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.38 % Favored : 92.54 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2480 helix: 1.02 (0.12), residues: 1930 sheet: None (None), residues: 0 loop : -3.80 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 144 TYR 0.031 0.002 TYR F 279 PHE 0.022 0.001 PHE G 55 TRP 0.012 0.001 TRP C 210 HIS 0.003 0.001 HIS I 245 Details of bonding type rmsd covalent geometry : bond 0.00285 (20010) covalent geometry : angle 0.73837 (27200) SS BOND : bond 0.00232 ( 30) SS BOND : angle 1.55707 ( 60) hydrogen bonds : bond 0.03681 ( 1311) hydrogen bonds : angle 4.17802 ( 3933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.30 seconds wall clock time: 56 minutes 26.55 seconds (3386.55 seconds total)