Starting phenix.real_space_refine on Tue Nov 19 11:53:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/11_2024/6ytv_10924.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/11_2024/6ytv_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/11_2024/6ytv_10924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/11_2024/6ytv_10924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/11_2024/6ytv_10924.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/11_2024/6ytv_10924.cif" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 5.97, per 1000 atoms: 0.31 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=3, 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 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: 5.32 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.61 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: 5.49 Time building geometry restraints manager: 6.14 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: 10517 17.73 - 35.46: 1110 35.46 - 53.19: 191 53.19 - 70.93: 11 70.93 - 88.66: 20 Dihedral angle restraints: 11849 sinusoidal: 4489 harmonic: 7360 Sorted by residual: dihedral pdb=" CB CYS A 43 " pdb=" SG CYS A 43 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.23 -65.77 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CA GLN J 271 " pdb=" C GLN J 271 " pdb=" N TYR J 272 " pdb=" CA TYR J 272 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLN A 271 " pdb=" C GLN A 271 " pdb=" N TYR A 272 " pdb=" CA TYR A 272 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 11846 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: 2.03 - 2.61: 268 2.61 - 3.18: 18975 3.18 - 3.75: 30715 3.75 - 4.33: 37968 4.33 - 4.90: 60087 Nonbonded interactions: 148013 Sorted by model distance: nonbonded pdb=" SG CYS E 41 " pdb=" SG CYS E 126 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 41 " pdb=" SG CYS B 126 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS I 41 " pdb=" SG CYS I 126 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS G 41 " pdb=" SG CYS G 126 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS H 41 " pdb=" SG CYS H 126 " model vdw 2.032 3.760 ... (remaining 148008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 37.460 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- 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 20010 Z= 0.276 Angle : 0.779 9.611 27200 Z= 0.413 Chirality : 0.043 0.254 3170 Planarity : 0.005 0.031 3350 Dihedral : 14.562 88.658 7080 Min Nonbonded Distance : 2.032 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.002 TRP J 113 HIS 0.004 0.002 HIS H 277 PHE 0.018 0.002 PHE I 266 TYR 0.014 0.002 TYR A 68 ARG 0.002 0.001 ARG E 32 *********************** 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 : 2.199 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: 0.8336 (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: 0.7560 (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: 0.7858 (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: 0.8539 (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: 0.8624 (tt) cc_final: 0.8197 (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: 0.8559 (pp20) cc_final: 0.8350 (pp20) REVERT: D 234 LYS cc_start: 0.8326 (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: 0.8372 (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: 0.8092 (mtt-85) cc_final: 0.7726 (mtt90) REVERT: F 231 GLU cc_start: 0.8756 (pp20) cc_final: 0.8288 (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: 0.8283 (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: 0.6885 (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: 0.7546 (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: 0.7700 (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: 0.7550 (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: 0.3345 time to fit residues: 385.7313 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 : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 75 optimal weight: 0.0980 chunk 119 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 C 277 HIS D 175 GLN D 216 GLN D 277 HIS E 216 GLN E 258 GLN E 277 HIS F 175 GLN F 216 GLN F 277 HIS 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.218 Angle : 0.713 7.426 27200 Z= 0.360 Chirality : 0.041 0.197 3170 Planarity : 0.005 0.055 3350 Dihedral : 5.234 24.218 2690 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2480 helix: 0.47 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.38 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 113 HIS 0.005 0.001 HIS A 245 PHE 0.012 0.002 PHE H 204 TYR 0.020 0.002 TYR G 279 ARG 0.008 0.001 ARG D 144 *********************** 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 743 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 1.988 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: A 32 ARG cc_start: 0.7157 (ttt-90) cc_final: 0.6934 (ttt90) REVERT: A 134 PHE cc_start: 0.8453 (t80) cc_final: 0.8042 (t80) REVERT: A 215 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8221 (tp30) REVERT: A 234 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7518 (ttpt) REVERT: A 235 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 236 ASN cc_start: 0.7903 (m110) cc_final: 0.7618 (m-40) REVERT: A 258 GLN cc_start: 0.8055 (tt0) cc_final: 0.7780 (tm-30) REVERT: B 32 ARG cc_start: 0.6509 (ttt-90) cc_final: 0.6175 (tpt170) REVERT: B 73 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7683 (tpp-160) REVERT: B 215 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8106 (tp30) REVERT: B 231 GLU cc_start: 0.8492 (pp20) cc_final: 0.8154 (pp20) REVERT: B 234 LYS cc_start: 0.8328 (ttmt) cc_final: 0.7704 (tttm) REVERT: B 235 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 236 ASN cc_start: 0.8004 (m110) cc_final: 0.7588 (m-40) REVERT: C 73 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7707 (tpp-160) REVERT: C 94 ARG cc_start: 0.5215 (ttm110) cc_final: 0.4962 (ptt180) REVERT: C 220 ILE cc_start: 0.8536 (tt) cc_final: 0.8299 (tt) REVERT: C 234 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7835 (ttpt) REVERT: C 235 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 236 ASN cc_start: 0.8098 (m110) cc_final: 0.7820 (m-40) REVERT: C 258 GLN cc_start: 0.8300 (tt0) cc_final: 0.7840 (tm-30) REVERT: C 267 ASN cc_start: 0.8188 (t0) cc_final: 0.7670 (t0) REVERT: D 32 ARG cc_start: 0.6405 (ttt-90) cc_final: 0.6187 (tpt170) REVERT: D 189 LEU cc_start: 0.8680 (tt) cc_final: 0.8287 (tp) REVERT: D 192 PHE cc_start: 0.8803 (t80) cc_final: 0.8601 (t80) REVERT: D 231 GLU cc_start: 0.8505 (pp20) cc_final: 0.8290 (pp20) REVERT: D 234 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7778 (ttpt) REVERT: D 256 GLU cc_start: 0.8295 (tt0) cc_final: 0.7975 (tt0) REVERT: D 267 ASN cc_start: 0.8289 (t0) cc_final: 0.7710 (t0) REVERT: D 282 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.6793 (mmm160) REVERT: E 32 ARG cc_start: 0.7251 (ttt-90) cc_final: 0.6697 (tpp-160) REVERT: E 41 CYS cc_start: 0.8020 (t) cc_final: 0.7265 (t) REVERT: E 73 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7653 (tpp-160) REVERT: E 125 GLU cc_start: 0.7565 (tp30) cc_final: 0.7267 (tp30) REVERT: E 126 CYS cc_start: 0.8221 (t) cc_final: 0.7324 (t) REVERT: E 231 GLU cc_start: 0.8497 (pp20) cc_final: 0.8077 (pp20) REVERT: E 234 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7688 (tttt) REVERT: E 235 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8191 (tm-30) REVERT: E 236 ASN cc_start: 0.7808 (m110) cc_final: 0.7531 (m110) REVERT: F 32 ARG cc_start: 0.7126 (ttt-90) cc_final: 0.6898 (ttt90) REVERT: F 94 ARG cc_start: 0.5201 (ttm110) cc_final: 0.4882 (ptt180) REVERT: F 125 GLU cc_start: 0.7707 (tp30) cc_final: 0.7395 (tp30) REVERT: F 166 LEU cc_start: 0.8078 (tt) cc_final: 0.7406 (mt) REVERT: F 234 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7505 (ttpt) REVERT: F 235 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8244 (tm-30) REVERT: F 236 ASN cc_start: 0.7909 (m110) cc_final: 0.7576 (m-40) REVERT: F 258 GLN cc_start: 0.8073 (tt0) cc_final: 0.7803 (tm-30) REVERT: G 32 ARG cc_start: 0.6698 (ttt-90) cc_final: 0.6273 (tpt170) REVERT: G 125 GLU cc_start: 0.7520 (tp30) cc_final: 0.7313 (tp30) REVERT: G 220 ILE cc_start: 0.8663 (tt) cc_final: 0.8365 (tt) REVERT: G 234 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7624 (ttpt) REVERT: H 94 ARG cc_start: 0.5159 (ttm110) cc_final: 0.4640 (ptt180) REVERT: H 125 GLU cc_start: 0.7552 (tp30) cc_final: 0.7346 (tp30) REVERT: H 234 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7658 (ttpt) REVERT: H 267 ASN cc_start: 0.8224 (t0) cc_final: 0.7726 (t0) REVERT: I 32 ARG cc_start: 0.7008 (ttt-90) cc_final: 0.6459 (tpt170) REVERT: I 208 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8092 (mtpt) REVERT: I 224 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8043 (ttpt) REVERT: I 231 GLU cc_start: 0.8504 (pp20) cc_final: 0.8131 (pp20) REVERT: I 234 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7779 (ttpt) REVERT: I 256 GLU cc_start: 0.8308 (tt0) cc_final: 0.8065 (tt0) REVERT: I 267 ASN cc_start: 0.8572 (t0) cc_final: 0.7960 (t0) REVERT: I 279 TYR cc_start: 0.7910 (t80) cc_final: 0.7590 (t80) REVERT: J 32 ARG cc_start: 0.7103 (ttt-90) cc_final: 0.6825 (ttt90) REVERT: J 73 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7416 (tpp-160) REVERT: J 94 ARG cc_start: 0.5371 (ttm110) cc_final: 0.4926 (ptt180) REVERT: J 125 GLU cc_start: 0.7449 (tp30) cc_final: 0.7115 (tp30) REVERT: J 205 LEU cc_start: 0.9062 (tp) cc_final: 0.8830 (tp) REVERT: J 231 GLU cc_start: 0.8524 (pp20) cc_final: 0.8306 (tm-30) REVERT: J 234 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7628 (tttt) REVERT: J 235 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8311 (tm-30) REVERT: J 282 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6790 (mmm160) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.3069 time to fit residues: 345.6566 Evaluate side-chains 595 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 227 optimal weight: 0.0020 chunk 245 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 225 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN C 245 HIS ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20010 Z= 0.190 Angle : 0.700 10.188 27200 Z= 0.344 Chirality : 0.040 0.278 3170 Planarity : 0.005 0.044 3350 Dihedral : 4.944 24.053 2690 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2480 helix: 0.93 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.50 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 113 HIS 0.007 0.001 HIS H 277 PHE 0.021 0.002 PHE J 241 TYR 0.029 0.002 TYR A 51 ARG 0.007 0.000 ARG E 144 *********************** 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 770 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 769 time to evaluate : 1.689 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: A 32 ARG cc_start: 0.7147 (ttt-90) cc_final: 0.6854 (ttt90) REVERT: A 125 GLU cc_start: 0.7641 (tp30) cc_final: 0.7301 (tp30) REVERT: A 166 LEU cc_start: 0.8173 (tt) cc_final: 0.7394 (mt) REVERT: A 206 GLN cc_start: 0.8748 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 210 TRP cc_start: 0.8930 (t60) cc_final: 0.8695 (t60) REVERT: A 219 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7091 (tm-30) REVERT: A 220 ILE cc_start: 0.8872 (tt) cc_final: 0.8367 (tt) REVERT: A 234 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7552 (ttpt) REVERT: A 235 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 236 ASN cc_start: 0.7861 (m110) cc_final: 0.7529 (m-40) REVERT: A 258 GLN cc_start: 0.8177 (tt0) cc_final: 0.7948 (tm-30) REVERT: A 274 SER cc_start: 0.7833 (p) cc_final: 0.7616 (p) REVERT: A 278 LYS cc_start: 0.7892 (tttt) cc_final: 0.7688 (ttmt) REVERT: B 73 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7655 (tpp-160) REVERT: B 125 GLU cc_start: 0.7726 (tp30) cc_final: 0.7477 (tp30) REVERT: B 159 LYS cc_start: 0.6872 (mttt) cc_final: 0.6542 (mmtp) REVERT: B 215 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 220 ILE cc_start: 0.8462 (tt) cc_final: 0.7935 (tt) REVERT: B 234 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7685 (tttm) REVERT: B 236 ASN cc_start: 0.7727 (m110) cc_final: 0.7367 (m110) REVERT: C 94 ARG cc_start: 0.5285 (ttm110) cc_final: 0.4890 (ptt180) REVERT: C 134 PHE cc_start: 0.8337 (t80) cc_final: 0.7870 (t80) REVERT: C 210 TRP cc_start: 0.8781 (t60) cc_final: 0.8573 (t60) REVERT: C 220 ILE cc_start: 0.8512 (tt) cc_final: 0.8162 (tt) REVERT: C 234 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7805 (ttpt) REVERT: C 235 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 236 ASN cc_start: 0.8049 (m110) cc_final: 0.7818 (m-40) REVERT: C 258 GLN cc_start: 0.8256 (tt0) cc_final: 0.7900 (tm-30) REVERT: D 32 ARG cc_start: 0.6625 (ttt-90) cc_final: 0.6110 (tpt170) REVERT: D 68 TYR cc_start: 0.7334 (t80) cc_final: 0.7093 (t80) REVERT: D 189 LEU cc_start: 0.8656 (tt) cc_final: 0.8272 (tp) REVERT: D 192 PHE cc_start: 0.8767 (t80) cc_final: 0.8523 (t80) REVERT: D 205 LEU cc_start: 0.9257 (tp) cc_final: 0.9016 (tp) REVERT: D 231 GLU cc_start: 0.8450 (pp20) cc_final: 0.8247 (pp20) REVERT: D 234 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7707 (ttpt) REVERT: D 267 ASN cc_start: 0.8388 (t0) cc_final: 0.7742 (t0) REVERT: E 32 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.6725 (tpp-160) REVERT: E 73 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.7618 (tpp-160) REVERT: E 226 THR cc_start: 0.8302 (m) cc_final: 0.7919 (p) REVERT: E 231 GLU cc_start: 0.8459 (pp20) cc_final: 0.8189 (tm-30) REVERT: E 234 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7684 (tttt) REVERT: E 235 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 236 ASN cc_start: 0.7801 (m110) cc_final: 0.7562 (m-40) REVERT: E 279 TYR cc_start: 0.7937 (t80) cc_final: 0.7737 (t80) REVERT: F 125 GLU cc_start: 0.7718 (tp30) cc_final: 0.7338 (tp30) REVERT: F 144 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8178 (ttp80) REVERT: F 146 CYS cc_start: 0.8127 (m) cc_final: 0.7801 (m) REVERT: F 166 LEU cc_start: 0.7987 (tt) cc_final: 0.7448 (mt) REVERT: F 206 GLN cc_start: 0.8756 (tt0) cc_final: 0.7948 (tm-30) REVERT: F 210 TRP cc_start: 0.8880 (t60) cc_final: 0.8613 (t60) REVERT: F 234 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7427 (ttpt) REVERT: F 235 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8221 (tm-30) REVERT: F 236 ASN cc_start: 0.7479 (m110) cc_final: 0.6944 (m-40) REVERT: F 278 LYS cc_start: 0.7910 (tttt) cc_final: 0.7351 (ttmt) REVERT: G 32 ARG cc_start: 0.6586 (ttt-90) cc_final: 0.6102 (tpt170) REVERT: G 73 ARG cc_start: 0.5197 (tpp-160) cc_final: 0.4344 (tpt170) REVERT: G 125 GLU cc_start: 0.7609 (tp30) cc_final: 0.7281 (tp30) REVERT: G 173 GLN cc_start: 0.8733 (mt0) cc_final: 0.7877 (mp10) REVERT: G 215 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7845 (tp30) REVERT: G 220 ILE cc_start: 0.8593 (tt) cc_final: 0.8354 (tt) REVERT: G 224 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7795 (ttpt) REVERT: G 236 ASN cc_start: 0.7403 (m-40) cc_final: 0.7072 (m-40) REVERT: H 94 ARG cc_start: 0.5078 (ttm110) cc_final: 0.4634 (ptt180) REVERT: H 125 GLU cc_start: 0.7688 (tp30) cc_final: 0.7402 (tp30) REVERT: H 144 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8021 (tmm-80) REVERT: H 173 GLN cc_start: 0.8765 (mt0) cc_final: 0.8271 (mp10) REVERT: H 210 TRP cc_start: 0.8814 (t60) cc_final: 0.8584 (t60) REVERT: H 234 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7655 (ttpt) REVERT: I 32 ARG cc_start: 0.7010 (ttt-90) cc_final: 0.6326 (tpt170) REVERT: I 208 LYS cc_start: 0.8276 (mtpp) cc_final: 0.8013 (mtpt) REVERT: I 224 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8250 (ttpt) REVERT: I 231 GLU cc_start: 0.8377 (pp20) cc_final: 0.8166 (pp20) REVERT: I 234 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7569 (tttt) REVERT: J 32 ARG cc_start: 0.7047 (ttt-90) cc_final: 0.6807 (ttt90) REVERT: J 73 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.7553 (tpp-160) REVERT: J 94 ARG cc_start: 0.5125 (ttm110) cc_final: 0.4723 (ptt180) REVERT: J 125 GLU cc_start: 0.7716 (tp30) cc_final: 0.7437 (tp30) REVERT: J 134 PHE cc_start: 0.8666 (t80) cc_final: 0.8170 (t80) REVERT: J 217 GLU cc_start: 0.8342 (tt0) cc_final: 0.8003 (tt0) REVERT: J 234 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7606 (tttt) REVERT: J 235 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8370 (tm-30) REVERT: J 236 ASN cc_start: 0.7861 (m110) cc_final: 0.7602 (m-40) REVERT: J 282 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6775 (mmm160) outliers start: 1 outliers final: 0 residues processed: 770 average time/residue: 0.2995 time to fit residues: 352.8323 Evaluate side-chains 615 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 245 HIS ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20010 Z= 0.220 Angle : 0.706 8.579 27200 Z= 0.349 Chirality : 0.040 0.200 3170 Planarity : 0.005 0.046 3350 Dihedral : 4.807 23.774 2690 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2480 helix: 0.97 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.50 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 113 HIS 0.006 0.001 HIS B 245 PHE 0.017 0.002 PHE H 55 TYR 0.033 0.002 TYR A 51 ARG 0.009 0.001 ARG J 144 *********************** 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 747 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 747 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7191 (ttt-90) cc_final: 0.6833 (ttt90) REVERT: A 125 GLU cc_start: 0.7588 (tp30) cc_final: 0.7329 (tp30) REVERT: A 144 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7927 (tmm-80) REVERT: A 210 TRP cc_start: 0.8957 (t60) cc_final: 0.8756 (t60) REVERT: A 234 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7596 (ttpt) REVERT: A 235 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 236 ASN cc_start: 0.7847 (m110) cc_final: 0.7571 (m-40) REVERT: A 274 SER cc_start: 0.8420 (p) cc_final: 0.7900 (p) REVERT: B 32 ARG cc_start: 0.6564 (ttt-90) cc_final: 0.6106 (tpt170) REVERT: B 73 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7647 (tpp-160) REVERT: B 125 GLU cc_start: 0.7649 (tp30) cc_final: 0.7327 (tp30) REVERT: B 159 LYS cc_start: 0.6759 (mttt) cc_final: 0.6406 (mmtp) REVERT: B 215 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7748 (tp30) REVERT: B 234 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7629 (tttm) REVERT: B 279 TYR cc_start: 0.7946 (t80) cc_final: 0.7697 (t80) REVERT: C 63 LEU cc_start: 0.8882 (tp) cc_final: 0.8651 (tp) REVERT: C 94 ARG cc_start: 0.5233 (ttm110) cc_final: 0.4673 (ptt180) REVERT: C 125 GLU cc_start: 0.7566 (tp30) cc_final: 0.7361 (tp30) REVERT: C 134 PHE cc_start: 0.8342 (t80) cc_final: 0.7952 (t80) REVERT: C 220 ILE cc_start: 0.8497 (tt) cc_final: 0.8278 (tt) REVERT: C 234 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7879 (ttpt) REVERT: C 235 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8250 (tm-30) REVERT: C 236 ASN cc_start: 0.8041 (m110) cc_final: 0.7761 (m110) REVERT: C 258 GLN cc_start: 0.8337 (tt0) cc_final: 0.7969 (tm-30) REVERT: C 278 LYS cc_start: 0.8295 (tttt) cc_final: 0.7883 (ttpt) REVERT: D 32 ARG cc_start: 0.6500 (ttt-90) cc_final: 0.6284 (tpt170) REVERT: D 68 TYR cc_start: 0.7332 (t80) cc_final: 0.7074 (t80) REVERT: D 144 ARG cc_start: 0.8558 (tmm-80) cc_final: 0.8355 (ttp80) REVERT: D 177 LEU cc_start: 0.9241 (tp) cc_final: 0.8964 (tp) REVERT: D 189 LEU cc_start: 0.8647 (tt) cc_final: 0.8201 (tp) REVERT: D 192 PHE cc_start: 0.8770 (t80) cc_final: 0.8549 (t80) REVERT: D 234 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7770 (tttt) REVERT: D 267 ASN cc_start: 0.8346 (t0) cc_final: 0.7627 (t0) REVERT: D 279 TYR cc_start: 0.8072 (t80) cc_final: 0.7763 (t80) REVERT: E 32 ARG cc_start: 0.7428 (ttt-90) cc_final: 0.6764 (tpp-160) REVERT: E 73 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7596 (tpp-160) REVERT: E 118 LEU cc_start: 0.8547 (tp) cc_final: 0.8345 (tp) REVERT: E 205 LEU cc_start: 0.9149 (tp) cc_final: 0.8735 (tp) REVERT: E 217 GLU cc_start: 0.8360 (tt0) cc_final: 0.8018 (tt0) REVERT: E 231 GLU cc_start: 0.8352 (pp20) cc_final: 0.8129 (tm-30) REVERT: E 234 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7703 (tttt) REVERT: E 235 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 256 GLU cc_start: 0.8800 (tt0) cc_final: 0.8554 (tt0) REVERT: E 278 LYS cc_start: 0.8260 (tttt) cc_final: 0.7731 (ttmt) REVERT: E 279 TYR cc_start: 0.7977 (t80) cc_final: 0.7681 (t80) REVERT: F 125 GLU cc_start: 0.7752 (tp30) cc_final: 0.7370 (tp30) REVERT: F 134 PHE cc_start: 0.8453 (t80) cc_final: 0.8205 (t80) REVERT: F 144 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8217 (ttp80) REVERT: F 146 CYS cc_start: 0.8233 (m) cc_final: 0.8002 (m) REVERT: F 206 GLN cc_start: 0.8897 (tt0) cc_final: 0.8115 (tm-30) REVERT: F 210 TRP cc_start: 0.8861 (t60) cc_final: 0.8627 (t60) REVERT: F 234 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7459 (ttpt) REVERT: F 235 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8170 (tm-30) REVERT: F 236 ASN cc_start: 0.7619 (m110) cc_final: 0.7042 (m-40) REVERT: G 32 ARG cc_start: 0.6749 (ttt-90) cc_final: 0.6191 (tpt170) REVERT: G 125 GLU cc_start: 0.7694 (tp30) cc_final: 0.7267 (tp30) REVERT: G 173 GLN cc_start: 0.8867 (mt0) cc_final: 0.7992 (mp10) REVERT: G 215 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7850 (tp30) REVERT: G 220 ILE cc_start: 0.8611 (tt) cc_final: 0.8356 (tt) REVERT: G 224 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7917 (ttpt) REVERT: H 32 ARG cc_start: 0.6766 (ttt-90) cc_final: 0.5927 (tpt170) REVERT: H 94 ARG cc_start: 0.5106 (ttm110) cc_final: 0.4728 (ptt180) REVERT: H 125 GLU cc_start: 0.7786 (tp30) cc_final: 0.7492 (tp30) REVERT: H 134 PHE cc_start: 0.8420 (t80) cc_final: 0.8203 (t80) REVERT: H 144 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7938 (tmm-80) REVERT: H 210 TRP cc_start: 0.8833 (t60) cc_final: 0.8623 (t60) REVERT: H 220 ILE cc_start: 0.8619 (tt) cc_final: 0.8381 (tt) REVERT: H 234 LYS cc_start: 0.8350 (ttmt) cc_final: 0.7562 (ttpt) REVERT: H 267 ASN cc_start: 0.8185 (t0) cc_final: 0.7681 (t0) REVERT: I 32 ARG cc_start: 0.7042 (ttt-90) cc_final: 0.6228 (tpt170) REVERT: I 205 LEU cc_start: 0.9179 (tp) cc_final: 0.8941 (tp) REVERT: I 208 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8021 (mtmt) REVERT: I 224 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7996 (ttpt) REVERT: I 234 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7587 (tttt) REVERT: J 32 ARG cc_start: 0.7220 (ttt-90) cc_final: 0.6749 (ttt90) REVERT: J 63 LEU cc_start: 0.9005 (tp) cc_final: 0.8777 (tp) REVERT: J 73 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7568 (tpp-160) REVERT: J 94 ARG cc_start: 0.5069 (ttm110) cc_final: 0.4659 (ptt180) REVERT: J 125 GLU cc_start: 0.7662 (tp30) cc_final: 0.7343 (tp30) REVERT: J 205 LEU cc_start: 0.9113 (tp) cc_final: 0.8826 (tp) REVERT: J 217 GLU cc_start: 0.8486 (tt0) cc_final: 0.8181 (tt0) REVERT: J 220 ILE cc_start: 0.8415 (tt) cc_final: 0.8155 (tt) REVERT: J 234 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7768 (tttt) REVERT: J 278 LYS cc_start: 0.8232 (tttt) cc_final: 0.7696 (ttmt) outliers start: 0 outliers final: 0 residues processed: 747 average time/residue: 0.3074 time to fit residues: 350.5079 Evaluate side-chains 610 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS C 175 GLN C 245 HIS ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN I 175 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20010 Z= 0.233 Angle : 0.712 7.914 27200 Z= 0.353 Chirality : 0.041 0.193 3170 Planarity : 0.005 0.048 3350 Dihedral : 4.794 23.448 2690 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2480 helix: 1.02 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.43 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 210 HIS 0.007 0.001 HIS A 245 PHE 0.017 0.002 PHE B 134 TYR 0.036 0.002 TYR D 51 ARG 0.010 0.001 ARG I 144 *********************** 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 743 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.6841 (ttt90) REVERT: A 73 ARG cc_start: 0.5554 (tpp-160) cc_final: 0.4530 (tpt170) REVERT: A 144 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7930 (tmm-80) REVERT: A 166 LEU cc_start: 0.8167 (tt) cc_final: 0.7461 (mt) REVERT: A 210 TRP cc_start: 0.8953 (t60) cc_final: 0.8724 (t60) REVERT: A 217 GLU cc_start: 0.8627 (tt0) cc_final: 0.8287 (tt0) REVERT: A 219 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 220 ILE cc_start: 0.8956 (tt) cc_final: 0.8650 (tt) REVERT: A 234 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7570 (ttpt) REVERT: A 235 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 236 ASN cc_start: 0.7851 (m110) cc_final: 0.7603 (m-40) REVERT: A 267 ASN cc_start: 0.8339 (t0) cc_final: 0.8026 (t0) REVERT: B 32 ARG cc_start: 0.6683 (ttt-90) cc_final: 0.6075 (tpt170) REVERT: B 73 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7634 (tpp-160) REVERT: B 215 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 231 GLU cc_start: 0.8332 (pp20) cc_final: 0.8121 (tm-30) REVERT: B 234 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7632 (tttm) REVERT: C 51 TYR cc_start: 0.8698 (t80) cc_final: 0.8405 (t80) REVERT: C 94 ARG cc_start: 0.5371 (ttm110) cc_final: 0.4730 (ptt180) REVERT: C 177 LEU cc_start: 0.9035 (tp) cc_final: 0.8719 (tp) REVERT: C 220 ILE cc_start: 0.8337 (tt) cc_final: 0.8092 (tt) REVERT: C 234 LYS cc_start: 0.8531 (ttmt) cc_final: 0.7866 (ttpt) REVERT: C 235 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 258 GLN cc_start: 0.8272 (tt0) cc_final: 0.7831 (tm-30) REVERT: D 32 ARG cc_start: 0.6550 (ttt-90) cc_final: 0.6291 (tpt170) REVERT: D 51 TYR cc_start: 0.8977 (t80) cc_final: 0.8753 (t80) REVERT: D 125 GLU cc_start: 0.7670 (tp30) cc_final: 0.7381 (tp30) REVERT: D 177 LEU cc_start: 0.9226 (tp) cc_final: 0.8934 (tp) REVERT: D 205 LEU cc_start: 0.9266 (tp) cc_final: 0.9061 (tp) REVERT: D 217 GLU cc_start: 0.8568 (tt0) cc_final: 0.8361 (tt0) REVERT: D 234 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7678 (tttt) REVERT: D 267 ASN cc_start: 0.8364 (t0) cc_final: 0.7571 (t0) REVERT: D 279 TYR cc_start: 0.7948 (t80) cc_final: 0.7727 (t80) REVERT: E 32 ARG cc_start: 0.7287 (ttt-90) cc_final: 0.6799 (tpp-160) REVERT: E 55 PHE cc_start: 0.8954 (m-80) cc_final: 0.8748 (m-10) REVERT: E 73 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7545 (tpp-160) REVERT: E 134 PHE cc_start: 0.8319 (t80) cc_final: 0.8107 (t80) REVERT: E 205 LEU cc_start: 0.9129 (tp) cc_final: 0.8777 (tp) REVERT: E 217 GLU cc_start: 0.8501 (tt0) cc_final: 0.8116 (tt0) REVERT: E 234 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7745 (tttt) REVERT: E 256 GLU cc_start: 0.8752 (tt0) cc_final: 0.8414 (tt0) REVERT: E 279 TYR cc_start: 0.7943 (t80) cc_final: 0.7630 (t80) REVERT: F 73 ARG cc_start: 0.5512 (tpp-160) cc_final: 0.4585 (tpt170) REVERT: F 125 GLU cc_start: 0.7722 (tp30) cc_final: 0.7331 (tp30) REVERT: F 144 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8215 (ttp80) REVERT: F 146 CYS cc_start: 0.8282 (m) cc_final: 0.8073 (m) REVERT: F 206 GLN cc_start: 0.8893 (tt0) cc_final: 0.7933 (tm-30) REVERT: F 210 TRP cc_start: 0.8927 (t60) cc_final: 0.8701 (t60) REVERT: F 219 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 220 ILE cc_start: 0.8843 (tt) cc_final: 0.8587 (tt) REVERT: F 234 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7531 (ttpt) REVERT: F 235 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8434 (tm-30) REVERT: F 279 TYR cc_start: 0.7757 (t80) cc_final: 0.7485 (t80) REVERT: G 32 ARG cc_start: 0.6611 (ttt-90) cc_final: 0.6287 (tpt170) REVERT: G 125 GLU cc_start: 0.7754 (tp30) cc_final: 0.7327 (tp30) REVERT: G 173 GLN cc_start: 0.8933 (mt0) cc_final: 0.7932 (mp10) REVERT: G 215 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7995 (tp30) REVERT: G 220 ILE cc_start: 0.8677 (tt) cc_final: 0.8459 (tt) REVERT: G 224 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7867 (ttpt) REVERT: G 226 THR cc_start: 0.8395 (m) cc_final: 0.8158 (p) REVERT: G 234 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7701 (tttm) REVERT: G 274 SER cc_start: 0.7695 (p) cc_final: 0.7391 (p) REVERT: H 32 ARG cc_start: 0.6809 (ttt-90) cc_final: 0.5956 (tpt170) REVERT: H 94 ARG cc_start: 0.5076 (ttm110) cc_final: 0.4527 (ptt180) REVERT: H 134 PHE cc_start: 0.8499 (t80) cc_final: 0.8220 (t80) REVERT: H 144 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8025 (tmm-80) REVERT: H 220 ILE cc_start: 0.8548 (tt) cc_final: 0.8177 (tt) REVERT: H 224 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7888 (ttpt) REVERT: H 234 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7590 (ttpt) REVERT: H 267 ASN cc_start: 0.8091 (t0) cc_final: 0.7664 (t0) REVERT: H 279 TYR cc_start: 0.7713 (t80) cc_final: 0.7467 (t80) REVERT: I 32 ARG cc_start: 0.6978 (ttt-90) cc_final: 0.6457 (tpt170) REVERT: I 208 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8102 (mtmt) REVERT: I 217 GLU cc_start: 0.8682 (tt0) cc_final: 0.8455 (tt0) REVERT: I 224 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8279 (ttpt) REVERT: I 234 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7490 (ttpt) REVERT: I 236 ASN cc_start: 0.8168 (m-40) cc_final: 0.7907 (m-40) REVERT: I 267 ASN cc_start: 0.8341 (t0) cc_final: 0.7667 (t0) REVERT: J 32 ARG cc_start: 0.7246 (ttt-90) cc_final: 0.6735 (ttt90) REVERT: J 63 LEU cc_start: 0.9007 (tp) cc_final: 0.8751 (tp) REVERT: J 73 ARG cc_start: 0.8013 (ttp-110) cc_final: 0.7534 (tpp-160) REVERT: J 94 ARG cc_start: 0.5170 (ttm110) cc_final: 0.4741 (ptt180) REVERT: J 134 PHE cc_start: 0.8555 (t80) cc_final: 0.8186 (t80) REVERT: J 217 GLU cc_start: 0.8598 (tt0) cc_final: 0.8158 (tt0) REVERT: J 234 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7665 (tttt) REVERT: J 278 LYS cc_start: 0.8152 (tttt) cc_final: 0.7886 (ttmt) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.3059 time to fit residues: 345.8195 Evaluate side-chains 610 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN G 258 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20010 Z= 0.283 Angle : 0.751 8.357 27200 Z= 0.376 Chirality : 0.043 0.192 3170 Planarity : 0.005 0.052 3350 Dihedral : 4.919 23.106 2690 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.10 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2480 helix: 0.90 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.36 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 210 HIS 0.006 0.001 HIS C 245 PHE 0.024 0.002 PHE J 55 TYR 0.028 0.003 TYR A 279 ARG 0.010 0.001 ARG E 144 *********************** 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 725 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 2.111 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6722 (ttt90) REVERT: A 63 LEU cc_start: 0.8880 (tp) cc_final: 0.8645 (tp) REVERT: A 125 GLU cc_start: 0.7579 (tp30) cc_final: 0.7168 (tp30) REVERT: A 166 LEU cc_start: 0.8171 (tt) cc_final: 0.7447 (mt) REVERT: A 210 TRP cc_start: 0.9017 (t60) cc_final: 0.8804 (t60) REVERT: A 234 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7502 (ttpt) REVERT: A 235 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 236 ASN cc_start: 0.7728 (m110) cc_final: 0.7439 (m110) REVERT: A 267 ASN cc_start: 0.8445 (t0) cc_final: 0.8196 (t0) REVERT: B 32 ARG cc_start: 0.6745 (ttt-90) cc_final: 0.6095 (tpt170) REVERT: B 73 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7579 (tpp-160) REVERT: B 125 GLU cc_start: 0.7462 (tp30) cc_final: 0.6824 (tp30) REVERT: B 215 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 231 GLU cc_start: 0.8357 (pp20) cc_final: 0.8045 (tm-30) REVERT: B 234 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7623 (tttm) REVERT: B 256 GLU cc_start: 0.8698 (tt0) cc_final: 0.8430 (tt0) REVERT: B 274 SER cc_start: 0.7702 (p) cc_final: 0.7408 (p) REVERT: B 275 MET cc_start: 0.7714 (mmp) cc_final: 0.7395 (mmt) REVERT: B 278 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7499 (tptt) REVERT: B 279 TYR cc_start: 0.8075 (t80) cc_final: 0.7777 (t80) REVERT: C 94 ARG cc_start: 0.5280 (ttm110) cc_final: 0.4674 (ptt180) REVERT: C 177 LEU cc_start: 0.9077 (tp) cc_final: 0.8759 (tp) REVERT: C 197 ARG cc_start: 0.8191 (mmt90) cc_final: 0.7875 (mtm-85) REVERT: C 220 ILE cc_start: 0.8449 (tt) cc_final: 0.8183 (tt) REVERT: C 234 LYS cc_start: 0.8456 (ttmt) cc_final: 0.7658 (ttpt) REVERT: D 32 ARG cc_start: 0.6800 (ttt-90) cc_final: 0.6373 (tpt170) REVERT: D 51 TYR cc_start: 0.8773 (t80) cc_final: 0.8437 (t80) REVERT: D 63 LEU cc_start: 0.8920 (tp) cc_final: 0.8719 (tp) REVERT: D 111 LEU cc_start: 0.8554 (mt) cc_final: 0.8352 (mt) REVERT: D 118 LEU cc_start: 0.8586 (tp) cc_final: 0.8376 (tp) REVERT: D 125 GLU cc_start: 0.7607 (tp30) cc_final: 0.7362 (tp30) REVERT: D 134 PHE cc_start: 0.8634 (t80) cc_final: 0.8142 (t80) REVERT: D 144 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8370 (ttp80) REVERT: D 231 GLU cc_start: 0.8402 (pp20) cc_final: 0.7815 (pp20) REVERT: D 234 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7645 (tttt) REVERT: D 267 ASN cc_start: 0.8235 (t0) cc_final: 0.7563 (t0) REVERT: D 279 TYR cc_start: 0.7951 (t80) cc_final: 0.7744 (t80) REVERT: E 32 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.6738 (ttt90) REVERT: E 73 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7609 (tpp-160) REVERT: E 134 PHE cc_start: 0.8355 (t80) cc_final: 0.8126 (t80) REVERT: E 205 LEU cc_start: 0.9104 (tp) cc_final: 0.8740 (tp) REVERT: E 217 GLU cc_start: 0.8620 (tt0) cc_final: 0.8179 (tt0) REVERT: E 231 GLU cc_start: 0.8396 (pp20) cc_final: 0.7743 (pp20) REVERT: E 234 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7667 (tttt) REVERT: E 256 GLU cc_start: 0.8744 (tt0) cc_final: 0.8479 (tt0) REVERT: E 279 TYR cc_start: 0.7937 (t80) cc_final: 0.7548 (t80) REVERT: F 63 LEU cc_start: 0.8861 (tp) cc_final: 0.8627 (tp) REVERT: F 144 ARG cc_start: 0.8710 (ttp80) cc_final: 0.8301 (ttp80) REVERT: F 146 CYS cc_start: 0.8299 (m) cc_final: 0.8039 (m) REVERT: F 210 TRP cc_start: 0.9007 (t60) cc_final: 0.8773 (t60) REVERT: F 234 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7417 (ttpt) REVERT: F 267 ASN cc_start: 0.8498 (t0) cc_final: 0.8188 (t0) REVERT: F 279 TYR cc_start: 0.7741 (t80) cc_final: 0.7534 (t80) REVERT: G 32 ARG cc_start: 0.6889 (ttt-90) cc_final: 0.6354 (tpt170) REVERT: G 125 GLU cc_start: 0.7714 (tp30) cc_final: 0.7169 (tp30) REVERT: G 224 LYS cc_start: 0.8582 (ttmt) cc_final: 0.7970 (ttpt) REVERT: G 234 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7522 (tttm) REVERT: G 274 SER cc_start: 0.7524 (p) cc_final: 0.7257 (p) REVERT: H 32 ARG cc_start: 0.6669 (ttt-90) cc_final: 0.5919 (tpt170) REVERT: H 94 ARG cc_start: 0.5232 (ttm110) cc_final: 0.4584 (ptt180) REVERT: H 134 PHE cc_start: 0.8489 (t80) cc_final: 0.8254 (t80) REVERT: H 144 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8113 (tmm-80) REVERT: H 220 ILE cc_start: 0.8513 (tt) cc_final: 0.8243 (tt) REVERT: H 231 GLU cc_start: 0.8406 (pp20) cc_final: 0.7930 (pp20) REVERT: H 234 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7529 (ttpt) REVERT: H 267 ASN cc_start: 0.8064 (t0) cc_final: 0.7679 (t0) REVERT: I 51 TYR cc_start: 0.8925 (t80) cc_final: 0.8718 (t80) REVERT: I 63 LEU cc_start: 0.8975 (tp) cc_final: 0.8760 (tp) REVERT: I 111 LEU cc_start: 0.8489 (mt) cc_final: 0.8214 (mt) REVERT: I 125 GLU cc_start: 0.7692 (tp30) cc_final: 0.7217 (tp30) REVERT: I 134 PHE cc_start: 0.8661 (t80) cc_final: 0.8135 (t80) REVERT: I 208 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8045 (mtmt) REVERT: I 224 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8280 (ttpt) REVERT: I 231 GLU cc_start: 0.8457 (pp20) cc_final: 0.7871 (pp20) REVERT: I 234 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7596 (tttt) REVERT: I 267 ASN cc_start: 0.8406 (t0) cc_final: 0.7823 (t0) REVERT: I 274 SER cc_start: 0.7993 (p) cc_final: 0.7473 (p) REVERT: J 32 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.6733 (ttt90) REVERT: J 73 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7504 (tpp-160) REVERT: J 94 ARG cc_start: 0.5105 (ttm110) cc_final: 0.4713 (ptt180) REVERT: J 118 LEU cc_start: 0.8655 (tp) cc_final: 0.8452 (tp) REVERT: J 134 PHE cc_start: 0.8583 (t80) cc_final: 0.8329 (t80) REVERT: J 217 GLU cc_start: 0.8389 (tt0) cc_final: 0.8175 (tt0) REVERT: J 224 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8190 (ttpt) REVERT: J 234 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7669 (tttt) REVERT: J 267 ASN cc_start: 0.8195 (t0) cc_final: 0.7966 (t0) REVERT: J 274 SER cc_start: 0.7938 (p) cc_final: 0.6425 (p) outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.3111 time to fit residues: 340.2735 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 : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN C 175 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.198 Angle : 0.713 10.894 27200 Z= 0.348 Chirality : 0.040 0.170 3170 Planarity : 0.005 0.057 3350 Dihedral : 4.754 22.915 2690 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2480 helix: 1.11 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.22 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 210 HIS 0.006 0.001 HIS G 277 PHE 0.014 0.001 PHE F 55 TYR 0.026 0.002 TYR J 51 ARG 0.011 0.001 ARG C 144 *********************** 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 732 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 732 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7110 (ttt-90) cc_final: 0.6724 (ttt90) REVERT: A 125 GLU cc_start: 0.7420 (tp30) cc_final: 0.7099 (tp30) REVERT: A 144 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7810 (tmm-80) REVERT: A 166 LEU cc_start: 0.8088 (tt) cc_final: 0.7381 (mt) REVERT: A 206 GLN cc_start: 0.8833 (tt0) cc_final: 0.7972 (tp40) REVERT: A 210 TRP cc_start: 0.8939 (t60) cc_final: 0.8726 (t60) REVERT: A 217 GLU cc_start: 0.8687 (tt0) cc_final: 0.8379 (tt0) REVERT: A 234 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7474 (ttpt) REVERT: A 235 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 236 ASN cc_start: 0.7755 (m110) cc_final: 0.7539 (m110) REVERT: B 32 ARG cc_start: 0.6631 (ttt-90) cc_final: 0.6122 (tpt170) REVERT: B 73 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7633 (tpp-160) REVERT: B 215 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 231 GLU cc_start: 0.8337 (pp20) cc_final: 0.8108 (tm-30) REVERT: B 234 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7632 (tttm) REVERT: B 256 GLU cc_start: 0.8670 (tt0) cc_final: 0.8189 (tt0) REVERT: B 274 SER cc_start: 0.7755 (p) cc_final: 0.7493 (p) REVERT: B 275 MET cc_start: 0.7651 (mmp) cc_final: 0.7360 (mmt) REVERT: B 279 TYR cc_start: 0.7925 (t80) cc_final: 0.7423 (t80) REVERT: C 51 TYR cc_start: 0.8634 (t80) cc_final: 0.8347 (t80) REVERT: C 94 ARG cc_start: 0.5264 (ttm110) cc_final: 0.4607 (ptt180) REVERT: C 220 ILE cc_start: 0.8430 (tt) cc_final: 0.8164 (tt) REVERT: C 234 LYS cc_start: 0.8451 (ttmt) cc_final: 0.7605 (ttpt) REVERT: C 258 GLN cc_start: 0.8296 (tt0) cc_final: 0.7849 (tm-30) REVERT: D 32 ARG cc_start: 0.6715 (ttt-90) cc_final: 0.6381 (tpt170) REVERT: D 51 TYR cc_start: 0.8639 (t80) cc_final: 0.8333 (t80) REVERT: D 63 LEU cc_start: 0.8981 (tp) cc_final: 0.8761 (tp) REVERT: D 125 GLU cc_start: 0.7520 (tp30) cc_final: 0.7246 (tp30) REVERT: D 134 PHE cc_start: 0.8575 (t80) cc_final: 0.7981 (t80) REVERT: D 144 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8291 (ttp80) REVERT: D 217 GLU cc_start: 0.8597 (tt0) cc_final: 0.8327 (tt0) REVERT: D 231 GLU cc_start: 0.8373 (pp20) cc_final: 0.8129 (tm-30) REVERT: D 234 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7578 (tttt) REVERT: D 235 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8501 (tm-30) REVERT: D 267 ASN cc_start: 0.8250 (t0) cc_final: 0.7586 (t0) REVERT: E 32 ARG cc_start: 0.7326 (ttt-90) cc_final: 0.6715 (ttt90) REVERT: E 73 ARG cc_start: 0.7937 (ttp-110) cc_final: 0.7562 (tpp-160) REVERT: E 217 GLU cc_start: 0.8593 (tt0) cc_final: 0.8311 (tt0) REVERT: E 234 LYS cc_start: 0.8413 (ttmt) cc_final: 0.7648 (tttt) REVERT: E 256 GLU cc_start: 0.8769 (tt0) cc_final: 0.8407 (tt0) REVERT: E 279 TYR cc_start: 0.7963 (t80) cc_final: 0.7634 (t80) REVERT: F 125 GLU cc_start: 0.7474 (tp30) cc_final: 0.7195 (tp30) REVERT: F 144 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8315 (ttp80) REVERT: F 146 CYS cc_start: 0.8330 (m) cc_final: 0.8062 (m) REVERT: F 206 GLN cc_start: 0.8901 (tt0) cc_final: 0.7926 (tm-30) REVERT: F 210 TRP cc_start: 0.8890 (t60) cc_final: 0.8649 (t60) REVERT: F 234 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7211 (ttpt) REVERT: F 274 SER cc_start: 0.8268 (p) cc_final: 0.7561 (p) REVERT: F 279 TYR cc_start: 0.7587 (t80) cc_final: 0.7269 (t80) REVERT: G 32 ARG cc_start: 0.6785 (ttt-90) cc_final: 0.6286 (tpt170) REVERT: G 125 GLU cc_start: 0.7635 (tp30) cc_final: 0.7189 (tp30) REVERT: G 224 LYS cc_start: 0.8570 (ttmt) cc_final: 0.7922 (ttpt) REVERT: G 226 THR cc_start: 0.8405 (m) cc_final: 0.8159 (p) REVERT: G 234 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7603 (ttpt) REVERT: G 274 SER cc_start: 0.7800 (p) cc_final: 0.7405 (p) REVERT: G 281 ASN cc_start: 0.7371 (p0) cc_final: 0.6995 (p0) REVERT: H 32 ARG cc_start: 0.6535 (ttt-90) cc_final: 0.5943 (tpt170) REVERT: H 63 LEU cc_start: 0.8981 (tp) cc_final: 0.8775 (tp) REVERT: H 94 ARG cc_start: 0.5179 (ttm110) cc_final: 0.4555 (ptt180) REVERT: H 144 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8146 (ttp80) REVERT: H 220 ILE cc_start: 0.8503 (tt) cc_final: 0.8185 (tt) REVERT: H 231 GLU cc_start: 0.8332 (pp20) cc_final: 0.8094 (tm-30) REVERT: H 234 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7454 (ttpt) REVERT: H 236 ASN cc_start: 0.7813 (m110) cc_final: 0.6822 (m110) REVERT: H 267 ASN cc_start: 0.7852 (t0) cc_final: 0.7438 (t0) REVERT: I 111 LEU cc_start: 0.8450 (mt) cc_final: 0.8194 (mt) REVERT: I 125 GLU cc_start: 0.7652 (tp30) cc_final: 0.7112 (tp30) REVERT: I 134 PHE cc_start: 0.8578 (t80) cc_final: 0.8089 (t80) REVERT: I 173 GLN cc_start: 0.8984 (mt0) cc_final: 0.8036 (mt0) REVERT: I 208 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8047 (mtmt) REVERT: I 224 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8238 (ttpt) REVERT: I 231 GLU cc_start: 0.8401 (pp20) cc_final: 0.7883 (pp20) REVERT: I 234 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7418 (tttt) REVERT: I 235 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8459 (tm-30) REVERT: I 267 ASN cc_start: 0.8287 (t0) cc_final: 0.7644 (t0) REVERT: I 274 SER cc_start: 0.7958 (p) cc_final: 0.7425 (p) REVERT: J 32 ARG cc_start: 0.7064 (ttt-90) cc_final: 0.6749 (ttt90) REVERT: J 63 LEU cc_start: 0.9031 (tp) cc_final: 0.8814 (tp) REVERT: J 73 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7511 (tpp-160) REVERT: J 94 ARG cc_start: 0.5297 (ttm110) cc_final: 0.4766 (ptt180) REVERT: J 144 ARG cc_start: 0.8609 (tmm-80) cc_final: 0.8178 (ptm-80) REVERT: J 224 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8228 (ttpt) REVERT: J 234 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7645 (tttt) REVERT: J 235 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7822 (tm-30) REVERT: J 256 GLU cc_start: 0.8607 (tt0) cc_final: 0.8232 (tt0) REVERT: J 274 SER cc_start: 0.7937 (p) cc_final: 0.6712 (p) REVERT: J 279 TYR cc_start: 0.7988 (t80) cc_final: 0.7420 (t80) outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.3392 time to fit residues: 382.2055 Evaluate side-chains 610 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20010 Z= 0.201 Angle : 0.725 10.348 27200 Z= 0.350 Chirality : 0.042 0.283 3170 Planarity : 0.005 0.061 3350 Dihedral : 4.728 24.235 2690 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2480 helix: 1.11 (0.12), residues: 1910 sheet: None (None), residues: 0 loop : -3.25 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 257 HIS 0.005 0.001 HIS G 277 PHE 0.021 0.002 PHE F 64 TYR 0.030 0.002 TYR A 279 ARG 0.013 0.000 ARG C 144 *********************** 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 728 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 728 time to evaluate : 2.036 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7119 (ttt-90) cc_final: 0.6743 (ttt90) REVERT: A 125 GLU cc_start: 0.7396 (tp30) cc_final: 0.7157 (tp30) REVERT: A 144 ARG cc_start: 0.8460 (ttp80) cc_final: 0.7961 (tmm-80) REVERT: A 166 LEU cc_start: 0.7961 (tt) cc_final: 0.7219 (mt) REVERT: A 206 GLN cc_start: 0.8832 (tt0) cc_final: 0.7924 (tp40) REVERT: A 210 TRP cc_start: 0.8934 (t60) cc_final: 0.8694 (t60) REVERT: A 217 GLU cc_start: 0.8666 (tt0) cc_final: 0.8292 (tt0) REVERT: A 234 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7453 (ttpt) REVERT: A 235 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 236 ASN cc_start: 0.7867 (m110) cc_final: 0.7612 (m-40) REVERT: A 256 GLU cc_start: 0.8548 (tt0) cc_final: 0.7964 (tt0) REVERT: B 32 ARG cc_start: 0.6575 (ttt-90) cc_final: 0.6270 (tpt170) REVERT: B 73 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7652 (tpp-160) REVERT: B 159 LYS cc_start: 0.6708 (mttt) cc_final: 0.6354 (mmtp) REVERT: B 215 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8001 (tm-30) REVERT: B 234 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7604 (tttm) REVERT: B 256 GLU cc_start: 0.8663 (tt0) cc_final: 0.8357 (tt0) REVERT: B 274 SER cc_start: 0.7637 (p) cc_final: 0.7185 (p) REVERT: B 279 TYR cc_start: 0.7968 (t80) cc_final: 0.7573 (t80) REVERT: C 51 TYR cc_start: 0.8615 (t80) cc_final: 0.8315 (t80) REVERT: C 94 ARG cc_start: 0.5268 (ttm110) cc_final: 0.4617 (ptt180) REVERT: C 134 PHE cc_start: 0.8410 (t80) cc_final: 0.8014 (t80) REVERT: C 177 LEU cc_start: 0.8993 (tp) cc_final: 0.8671 (tp) REVERT: C 220 ILE cc_start: 0.8414 (tt) cc_final: 0.8146 (tt) REVERT: C 234 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7600 (ttpt) REVERT: C 235 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8312 (tm-30) REVERT: C 258 GLN cc_start: 0.8363 (tt0) cc_final: 0.7991 (tm-30) REVERT: D 32 ARG cc_start: 0.6717 (ttt-90) cc_final: 0.6110 (tpt170) REVERT: D 51 TYR cc_start: 0.8476 (t80) cc_final: 0.8099 (t80) REVERT: D 134 PHE cc_start: 0.8578 (t80) cc_final: 0.7995 (t80) REVERT: D 144 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8307 (ttp80) REVERT: D 231 GLU cc_start: 0.8355 (pp20) cc_final: 0.8097 (tm-30) REVERT: D 234 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7506 (tttt) REVERT: D 235 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8485 (tm-30) REVERT: D 267 ASN cc_start: 0.8291 (t0) cc_final: 0.7584 (t0) REVERT: E 32 ARG cc_start: 0.7342 (ttt-90) cc_final: 0.6719 (ttt90) REVERT: E 63 LEU cc_start: 0.9048 (tp) cc_final: 0.8848 (tp) REVERT: E 73 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7562 (tpp-160) REVERT: E 234 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7638 (tttt) REVERT: E 235 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7434 (tm-30) REVERT: E 236 ASN cc_start: 0.7522 (m-40) cc_final: 0.7035 (m110) REVERT: E 256 GLU cc_start: 0.8777 (tt0) cc_final: 0.8446 (tt0) REVERT: E 274 SER cc_start: 0.7977 (p) cc_final: 0.6932 (p) REVERT: E 279 TYR cc_start: 0.8043 (t80) cc_final: 0.7719 (t80) REVERT: F 125 GLU cc_start: 0.7514 (tp30) cc_final: 0.7178 (tp30) REVERT: F 144 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8304 (ttp80) REVERT: F 206 GLN cc_start: 0.8895 (tt0) cc_final: 0.8127 (tp40) REVERT: F 210 TRP cc_start: 0.8828 (t60) cc_final: 0.8559 (t60) REVERT: F 234 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7206 (ttpt) REVERT: F 274 SER cc_start: 0.8355 (p) cc_final: 0.7743 (p) REVERT: F 279 TYR cc_start: 0.7630 (t80) cc_final: 0.7330 (t80) REVERT: G 32 ARG cc_start: 0.6837 (ttt-90) cc_final: 0.6290 (tpt170) REVERT: G 125 GLU cc_start: 0.7632 (tp30) cc_final: 0.7118 (tp30) REVERT: G 224 LYS cc_start: 0.8580 (ttmt) cc_final: 0.7927 (ttpt) REVERT: G 226 THR cc_start: 0.8450 (m) cc_final: 0.8158 (p) REVERT: G 234 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7468 (ttpt) REVERT: G 274 SER cc_start: 0.7842 (p) cc_final: 0.7352 (p) REVERT: G 281 ASN cc_start: 0.7315 (p0) cc_final: 0.6962 (p0) REVERT: H 32 ARG cc_start: 0.6626 (ttt-90) cc_final: 0.5885 (tpt170) REVERT: H 63 LEU cc_start: 0.8869 (tp) cc_final: 0.8639 (tp) REVERT: H 94 ARG cc_start: 0.5182 (ttm110) cc_final: 0.4556 (ptt180) REVERT: H 125 GLU cc_start: 0.7532 (tp30) cc_final: 0.7271 (tp30) REVERT: H 144 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8057 (ttp80) REVERT: H 231 GLU cc_start: 0.8275 (pp20) cc_final: 0.8041 (tm-30) REVERT: H 234 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7423 (ttpt) REVERT: H 236 ASN cc_start: 0.7820 (m110) cc_final: 0.6985 (m110) REVERT: I 63 LEU cc_start: 0.8945 (tp) cc_final: 0.8728 (tp) REVERT: I 125 GLU cc_start: 0.7671 (tp30) cc_final: 0.7136 (tp30) REVERT: I 134 PHE cc_start: 0.8525 (t80) cc_final: 0.8106 (t80) REVERT: I 173 GLN cc_start: 0.8902 (mt0) cc_final: 0.8140 (mt0) REVERT: I 208 LYS cc_start: 0.8356 (mtpp) cc_final: 0.8065 (mtmt) REVERT: I 224 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8184 (ttpt) REVERT: I 231 GLU cc_start: 0.8393 (pp20) cc_final: 0.8168 (tm-30) REVERT: I 234 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7480 (tttt) REVERT: I 267 ASN cc_start: 0.8258 (t0) cc_final: 0.7587 (t0) REVERT: I 274 SER cc_start: 0.7903 (p) cc_final: 0.7324 (p) REVERT: I 279 TYR cc_start: 0.7556 (t80) cc_final: 0.7351 (t80) REVERT: J 32 ARG cc_start: 0.7150 (ttt-90) cc_final: 0.6645 (ttt90) REVERT: J 63 LEU cc_start: 0.9017 (tp) cc_final: 0.8799 (tp) REVERT: J 73 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7586 (tpp-160) REVERT: J 94 ARG cc_start: 0.5309 (ttm110) cc_final: 0.4829 (ptt180) REVERT: J 224 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8330 (ttpt) REVERT: J 234 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7680 (tttt) REVERT: J 256 GLU cc_start: 0.8533 (tt0) cc_final: 0.8094 (tt0) REVERT: J 274 SER cc_start: 0.7859 (p) cc_final: 0.7329 (p) REVERT: J 279 TYR cc_start: 0.7963 (t80) cc_final: 0.7298 (t80) outliers start: 0 outliers final: 0 residues processed: 728 average time/residue: 0.3208 time to fit residues: 354.5337 Evaluate side-chains 628 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 202 optimal weight: 0.3980 chunk 212 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20010 Z= 0.187 Angle : 0.716 10.146 27200 Z= 0.343 Chirality : 0.040 0.249 3170 Planarity : 0.005 0.062 3350 Dihedral : 4.649 24.442 2690 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2480 helix: 1.10 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -3.31 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 210 HIS 0.005 0.001 HIS C 277 PHE 0.020 0.001 PHE D 123 TYR 0.025 0.002 TYR A 279 ARG 0.014 0.001 ARG E 144 *********************** 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 747 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 747 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7031 (ttt-90) cc_final: 0.6650 (ttt90) REVERT: A 125 GLU cc_start: 0.7397 (tp30) cc_final: 0.7168 (tp30) REVERT: A 166 LEU cc_start: 0.7859 (tt) cc_final: 0.7185 (mt) REVERT: A 206 GLN cc_start: 0.8756 (tt0) cc_final: 0.7953 (tp40) REVERT: A 217 GLU cc_start: 0.8644 (tt0) cc_final: 0.8351 (tt0) REVERT: A 234 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7439 (ttpt) REVERT: A 235 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 236 ASN cc_start: 0.7897 (m110) cc_final: 0.7670 (m-40) REVERT: A 256 GLU cc_start: 0.8464 (tt0) cc_final: 0.7878 (tt0) REVERT: A 274 SER cc_start: 0.8161 (p) cc_final: 0.7003 (p) REVERT: B 32 ARG cc_start: 0.6576 (ttt-90) cc_final: 0.6281 (tpt170) REVERT: B 73 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7663 (tpp-160) REVERT: B 134 PHE cc_start: 0.8373 (t80) cc_final: 0.8125 (t80) REVERT: B 159 LYS cc_start: 0.6664 (mttt) cc_final: 0.6328 (mmtp) REVERT: B 215 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 234 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7441 (ttpt) REVERT: B 256 GLU cc_start: 0.8645 (tt0) cc_final: 0.8236 (tt0) REVERT: B 274 SER cc_start: 0.7627 (p) cc_final: 0.7259 (p) REVERT: B 278 LYS cc_start: 0.8047 (tptt) cc_final: 0.7222 (tttt) REVERT: B 279 TYR cc_start: 0.8020 (t80) cc_final: 0.7558 (t80) REVERT: C 94 ARG cc_start: 0.5230 (ttm110) cc_final: 0.4594 (ptt180) REVERT: C 134 PHE cc_start: 0.8400 (t80) cc_final: 0.7969 (t80) REVERT: C 177 LEU cc_start: 0.8984 (tp) cc_final: 0.8605 (tp) REVERT: C 220 ILE cc_start: 0.8365 (tt) cc_final: 0.8143 (tt) REVERT: C 234 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7528 (ttpt) REVERT: D 32 ARG cc_start: 0.6935 (ttt-90) cc_final: 0.6312 (tpt170) REVERT: D 51 TYR cc_start: 0.8487 (t80) cc_final: 0.8181 (t80) REVERT: D 63 LEU cc_start: 0.8992 (tp) cc_final: 0.8774 (tp) REVERT: D 134 PHE cc_start: 0.8377 (t80) cc_final: 0.7900 (t80) REVERT: D 144 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8397 (ttp80) REVERT: D 231 GLU cc_start: 0.8420 (pp20) cc_final: 0.8188 (tm-30) REVERT: D 234 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7560 (tttt) REVERT: D 235 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8518 (tm-30) REVERT: D 267 ASN cc_start: 0.8251 (t0) cc_final: 0.7632 (t0) REVERT: D 274 SER cc_start: 0.7956 (p) cc_final: 0.7517 (p) REVERT: E 32 ARG cc_start: 0.7131 (ttt-90) cc_final: 0.6738 (ttt90) REVERT: E 55 PHE cc_start: 0.8961 (m-80) cc_final: 0.8467 (m-10) REVERT: E 73 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7547 (tpp-160) REVERT: E 166 LEU cc_start: 0.7931 (tt) cc_final: 0.7190 (mt) REVERT: E 234 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7646 (tttt) REVERT: E 256 GLU cc_start: 0.8730 (tt0) cc_final: 0.8363 (tt0) REVERT: E 274 SER cc_start: 0.7877 (p) cc_final: 0.7404 (p) REVERT: E 279 TYR cc_start: 0.7947 (t80) cc_final: 0.7728 (t80) REVERT: F 125 GLU cc_start: 0.7456 (tp30) cc_final: 0.7100 (tp30) REVERT: F 144 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8337 (ttp80) REVERT: F 206 GLN cc_start: 0.8919 (tt0) cc_final: 0.8046 (tp40) REVERT: F 210 TRP cc_start: 0.8876 (t60) cc_final: 0.8666 (t60) REVERT: F 234 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7220 (ttpt) REVERT: F 274 SER cc_start: 0.7952 (p) cc_final: 0.7274 (p) REVERT: F 279 TYR cc_start: 0.7654 (t80) cc_final: 0.7280 (t80) REVERT: G 32 ARG cc_start: 0.6841 (ttt-90) cc_final: 0.6312 (tpt170) REVERT: G 125 GLU cc_start: 0.7562 (tp30) cc_final: 0.7063 (tp30) REVERT: G 224 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7701 (ttpt) REVERT: G 226 THR cc_start: 0.8415 (m) cc_final: 0.8161 (p) REVERT: G 234 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7381 (ttpt) REVERT: G 274 SER cc_start: 0.7770 (p) cc_final: 0.6768 (p) REVERT: H 32 ARG cc_start: 0.6652 (ttt-90) cc_final: 0.5874 (tpt170) REVERT: H 63 LEU cc_start: 0.8874 (tp) cc_final: 0.8618 (tp) REVERT: H 94 ARG cc_start: 0.5191 (ttm110) cc_final: 0.4546 (ptt180) REVERT: H 125 GLU cc_start: 0.7426 (tp30) cc_final: 0.7117 (tp30) REVERT: H 144 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8165 (ttp80) REVERT: H 166 LEU cc_start: 0.8298 (tt) cc_final: 0.7754 (mt) REVERT: H 220 ILE cc_start: 0.8492 (tt) cc_final: 0.8264 (tt) REVERT: H 231 GLU cc_start: 0.8174 (pp20) cc_final: 0.7920 (tm-30) REVERT: H 234 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7370 (ttpt) REVERT: H 236 ASN cc_start: 0.7621 (m110) cc_final: 0.6780 (m110) REVERT: H 274 SER cc_start: 0.7529 (p) cc_final: 0.6891 (p) REVERT: I 63 LEU cc_start: 0.8934 (tp) cc_final: 0.8714 (tp) REVERT: I 125 GLU cc_start: 0.7688 (tp30) cc_final: 0.7135 (tp30) REVERT: I 134 PHE cc_start: 0.8425 (t80) cc_final: 0.8063 (t80) REVERT: I 144 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8159 (tmm-80) REVERT: I 173 GLN cc_start: 0.8935 (mt0) cc_final: 0.8140 (mt0) REVERT: I 208 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8026 (mtmt) REVERT: I 224 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8170 (ttpt) REVERT: I 231 GLU cc_start: 0.8378 (pp20) cc_final: 0.8158 (tm-30) REVERT: I 234 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7523 (tttt) REVERT: I 267 ASN cc_start: 0.8224 (t0) cc_final: 0.7672 (t0) REVERT: I 274 SER cc_start: 0.7993 (p) cc_final: 0.7363 (p) REVERT: I 279 TYR cc_start: 0.7614 (t80) cc_final: 0.7397 (t80) REVERT: J 32 ARG cc_start: 0.7150 (ttt-90) cc_final: 0.6658 (ttt90) REVERT: J 55 PHE cc_start: 0.8874 (m-80) cc_final: 0.8622 (m-80) REVERT: J 63 LEU cc_start: 0.8975 (tp) cc_final: 0.8751 (tp) REVERT: J 73 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7592 (tpp-160) REVERT: J 94 ARG cc_start: 0.5363 (ttm110) cc_final: 0.4950 (ptt180) REVERT: J 144 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8157 (tmm-80) REVERT: J 224 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8170 (ttpt) REVERT: J 234 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7595 (tttt) REVERT: J 235 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7579 (tm-30) REVERT: J 236 ASN cc_start: 0.7616 (m110) cc_final: 0.7277 (m110) REVERT: J 256 GLU cc_start: 0.8567 (tt0) cc_final: 0.8096 (tt0) REVERT: J 279 TYR cc_start: 0.7994 (t80) cc_final: 0.7262 (t80) outliers start: 0 outliers final: 0 residues processed: 747 average time/residue: 0.3149 time to fit residues: 359.2956 Evaluate side-chains 646 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 0.0030 chunk 165 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 153 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 245 HIS ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.182 Angle : 0.719 9.349 27200 Z= 0.344 Chirality : 0.040 0.237 3170 Planarity : 0.005 0.058 3350 Dihedral : 4.576 24.741 2690 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2480 helix: 1.12 (0.12), residues: 1930 sheet: None (None), residues: 0 loop : -3.63 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 210 HIS 0.008 0.001 HIS C 245 PHE 0.022 0.002 PHE F 134 TYR 0.025 0.002 TYR A 279 ARG 0.016 0.001 ARG C 144 ********************** 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 755 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 755 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6917 (ttt-90) cc_final: 0.6646 (ttt90) REVERT: A 125 GLU cc_start: 0.7360 (tp30) cc_final: 0.7109 (tp30) REVERT: A 166 LEU cc_start: 0.7824 (tt) cc_final: 0.7163 (mt) REVERT: A 206 GLN cc_start: 0.8686 (tt0) cc_final: 0.7733 (tm-30) REVERT: A 217 GLU cc_start: 0.8668 (tt0) cc_final: 0.8408 (tt0) REVERT: A 234 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7415 (ttpt) REVERT: A 235 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 236 ASN cc_start: 0.7982 (m110) cc_final: 0.7726 (m-40) REVERT: A 256 GLU cc_start: 0.8670 (tt0) cc_final: 0.8144 (tt0) REVERT: A 274 SER cc_start: 0.8196 (p) cc_final: 0.7162 (p) REVERT: B 32 ARG cc_start: 0.6610 (ttt-90) cc_final: 0.6303 (tpt170) REVERT: B 134 PHE cc_start: 0.8401 (t80) cc_final: 0.8062 (t80) REVERT: B 159 LYS cc_start: 0.6623 (mttt) cc_final: 0.6263 (mmtp) REVERT: B 215 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7846 (tm-30) REVERT: B 234 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7588 (tttm) REVERT: B 256 GLU cc_start: 0.8686 (tt0) cc_final: 0.8155 (tt0) REVERT: B 274 SER cc_start: 0.7555 (p) cc_final: 0.7163 (p) REVERT: B 278 LYS cc_start: 0.7980 (tptt) cc_final: 0.7525 (mttt) REVERT: B 279 TYR cc_start: 0.8078 (t80) cc_final: 0.7529 (t80) REVERT: C 51 TYR cc_start: 0.8639 (t80) cc_final: 0.8313 (t80) REVERT: C 63 LEU cc_start: 0.8875 (tp) cc_final: 0.8659 (tp) REVERT: C 94 ARG cc_start: 0.5196 (ttm110) cc_final: 0.4595 (ptt180) REVERT: C 134 PHE cc_start: 0.8335 (t80) cc_final: 0.7981 (t80) REVERT: C 177 LEU cc_start: 0.9006 (tp) cc_final: 0.8627 (tp) REVERT: C 220 ILE cc_start: 0.8663 (tt) cc_final: 0.8271 (tt) REVERT: C 234 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7486 (ttpt) REVERT: D 32 ARG cc_start: 0.6919 (ttt-90) cc_final: 0.6364 (tpt170) REVERT: D 51 TYR cc_start: 0.8484 (t80) cc_final: 0.8186 (t80) REVERT: D 134 PHE cc_start: 0.8413 (t80) cc_final: 0.8011 (t80) REVERT: D 144 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8427 (ttp80) REVERT: D 231 GLU cc_start: 0.8357 (pp20) cc_final: 0.8139 (tm-30) REVERT: D 234 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7532 (tttt) REVERT: D 235 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 274 SER cc_start: 0.7926 (p) cc_final: 0.7406 (p) REVERT: E 32 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6768 (ttt90) REVERT: E 73 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7584 (tpp-160) REVERT: E 166 LEU cc_start: 0.7800 (tt) cc_final: 0.7068 (mt) REVERT: E 234 LYS cc_start: 0.8368 (ttmt) cc_final: 0.7681 (tttt) REVERT: E 235 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7621 (tm-30) REVERT: E 256 GLU cc_start: 0.8803 (tt0) cc_final: 0.8458 (tt0) REVERT: E 274 SER cc_start: 0.7648 (p) cc_final: 0.6884 (p) REVERT: F 125 GLU cc_start: 0.7295 (tp30) cc_final: 0.6930 (tp30) REVERT: F 144 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8335 (ttp80) REVERT: F 206 GLN cc_start: 0.8874 (tt0) cc_final: 0.8008 (tp40) REVERT: F 234 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7133 (ttpt) REVERT: F 274 SER cc_start: 0.7902 (p) cc_final: 0.7216 (p) REVERT: F 279 TYR cc_start: 0.7747 (t80) cc_final: 0.7374 (t80) REVERT: G 32 ARG cc_start: 0.6869 (ttt-90) cc_final: 0.6321 (tpt170) REVERT: G 224 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7824 (ttpt) REVERT: G 226 THR cc_start: 0.8548 (m) cc_final: 0.8171 (p) REVERT: G 234 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7429 (ttpt) REVERT: G 274 SER cc_start: 0.8062 (p) cc_final: 0.7395 (p) REVERT: H 32 ARG cc_start: 0.6635 (ttt-90) cc_final: 0.5924 (tpt170) REVERT: H 48 ASN cc_start: 0.8676 (m-40) cc_final: 0.8390 (m110) REVERT: H 63 LEU cc_start: 0.8843 (tp) cc_final: 0.8606 (tp) REVERT: H 94 ARG cc_start: 0.5047 (ttm110) cc_final: 0.4600 (ptt180) REVERT: H 125 GLU cc_start: 0.7342 (tp30) cc_final: 0.7006 (tp30) REVERT: H 134 PHE cc_start: 0.8506 (t80) cc_final: 0.8224 (t80) REVERT: H 144 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8177 (ttp80) REVERT: H 166 LEU cc_start: 0.8265 (tt) cc_final: 0.7743 (mt) REVERT: H 231 GLU cc_start: 0.7920 (pp20) cc_final: 0.7636 (tm-30) REVERT: H 234 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7286 (ttpt) REVERT: H 236 ASN cc_start: 0.7592 (m110) cc_final: 0.7050 (m-40) REVERT: I 125 GLU cc_start: 0.7674 (tp30) cc_final: 0.7147 (tp30) REVERT: I 134 PHE cc_start: 0.8402 (t80) cc_final: 0.8021 (t80) REVERT: I 144 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8181 (tmm-80) REVERT: I 192 PHE cc_start: 0.8597 (t80) cc_final: 0.8382 (t80) REVERT: I 217 GLU cc_start: 0.8812 (tt0) cc_final: 0.8445 (tt0) REVERT: I 224 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8222 (ttpt) REVERT: I 234 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7576 (tttt) REVERT: I 258 GLN cc_start: 0.8147 (tt0) cc_final: 0.7851 (tm-30) REVERT: I 279 TYR cc_start: 0.7664 (t80) cc_final: 0.7423 (t80) REVERT: J 32 ARG cc_start: 0.7197 (ttt-90) cc_final: 0.6660 (ttt90) REVERT: J 55 PHE cc_start: 0.8856 (m-80) cc_final: 0.8620 (m-80) REVERT: J 63 LEU cc_start: 0.8975 (tp) cc_final: 0.8730 (tp) REVERT: J 73 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7613 (tpp-160) REVERT: J 94 ARG cc_start: 0.5311 (ttm110) cc_final: 0.4893 (ptt180) REVERT: J 144 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8184 (tmm-80) REVERT: J 234 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7570 (tttt) REVERT: J 235 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7520 (tm-30) REVERT: J 236 ASN cc_start: 0.7740 (m110) cc_final: 0.7349 (m110) REVERT: J 256 GLU cc_start: 0.8552 (tt0) cc_final: 0.8003 (tt0) REVERT: J 274 SER cc_start: 0.7768 (p) cc_final: 0.7393 (p) REVERT: J 279 TYR cc_start: 0.7972 (t80) cc_final: 0.7252 (t80) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.2826 time to fit residues: 327.1592 Evaluate side-chains 639 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 198 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 203 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 236 ASN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 GLN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122176 restraints weight = 36797.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125479 restraints weight = 21617.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127830 restraints weight = 14279.290| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.186 Angle : 0.720 9.116 27200 Z= 0.345 Chirality : 0.040 0.231 3170 Planarity : 0.005 0.060 3350 Dihedral : 4.580 26.069 2690 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2480 helix: 1.09 (0.12), residues: 1930 sheet: None (None), residues: 0 loop : -3.56 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP I 210 HIS 0.003 0.001 HIS I 245 PHE 0.018 0.002 PHE F 64 TYR 0.025 0.002 TYR A 279 ARG 0.016 0.001 ARG E 144 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: