Starting phenix.real_space_refine on Thu Sep 26 07:36:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/09_2024/5aey_2850.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/09_2024/5aey_2850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/09_2024/5aey_2850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/09_2024/5aey_2850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/09_2024/5aey_2850.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aey_2850/09_2024/5aey_2850.cif" } resolution = 4.3 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 40 5.16 5 C 7950 2.51 5 N 2140 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "D" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "E" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.34, per 1000 atoms: 0.58 Number of scatterers: 12675 At special positions: 0 Unit cell: (78.11, 98.44, 181.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 15 15.00 O 2530 8.00 N 2140 7.00 C 7950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 42.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.942A pdb=" N GLN A 73 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.835A pdb=" N VAL A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.771A pdb=" N TYR A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.816A pdb=" N PHE A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 removed outlier: 3.800A pdb=" N ALA A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.752A pdb=" N GLU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 213 removed outlier: 3.538A pdb=" N ALA A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 244 through 268 removed outlier: 3.877A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 5.553A pdb=" N ASP A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.957A pdb=" N GLN B 73 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.832A pdb=" N VAL B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.747A pdb=" N TYR B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.816A pdb=" N PHE B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 removed outlier: 3.805A pdb=" N ALA B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 152' Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.751A pdb=" N GLU B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.572A pdb=" N ALA B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 228 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 244 through 268 removed outlier: 3.881A pdb=" N VAL B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 removed outlier: 5.554A pdb=" N ASP B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.957A pdb=" N GLN C 73 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.819A pdb=" N VAL C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.752A pdb=" N TYR C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.818A pdb=" N PHE C 126 " --> pdb=" O LYS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 removed outlier: 3.796A pdb=" N ALA C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.749A pdb=" N GLU C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.573A pdb=" N ALA C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 228 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 244 through 268 removed outlier: 3.859A pdb=" N VAL C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 294 removed outlier: 5.567A pdb=" N ASP C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.960A pdb=" N GLN D 73 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 88 removed outlier: 3.824A pdb=" N VAL D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.751A pdb=" N TYR D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.818A pdb=" N PHE D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 152 removed outlier: 3.791A pdb=" N ALA D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 152' Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.751A pdb=" N GLU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.579A pdb=" N ALA D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 231 through 237 Processing helix chain 'D' and resid 244 through 268 removed outlier: 3.853A pdb=" N VAL D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 removed outlier: 5.568A pdb=" N ASP D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.949A pdb=" N GLN E 73 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 removed outlier: 3.822A pdb=" N VAL E 79 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.751A pdb=" N TYR E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.817A pdb=" N PHE E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 152 removed outlier: 3.834A pdb=" N ALA E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 149 through 152' Processing helix chain 'E' and resid 153 through 159 removed outlier: 3.732A pdb=" N GLU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 213 removed outlier: 3.575A pdb=" N ALA E 205 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 228 Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 244 through 268 removed outlier: 3.854A pdb=" N VAL E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 261 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 294 removed outlier: 5.562A pdb=" N ASP E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA E 289 " --> pdb=" O LEU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 309 through 317 Processing sheet with id=AA, first strand: chain 'A' and resid 22 through 29 removed outlier: 5.514A pdb=" N GLN A 17 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU A 2 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 101 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP A 7 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 98 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 143 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N CYS A 100 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 145 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 102 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AC, first strand: chain 'A' and resid 187 through 194 removed outlier: 5.540A pdb=" N ILE A 188 " --> pdb=" O MET A 182 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET A 182 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 278 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 22 through 29 removed outlier: 5.454A pdb=" N GLN B 17 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 2 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 101 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 7 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 98 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 143 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N CYS B 100 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 145 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 102 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=BC, first strand: chain 'B' and resid 187 through 194 removed outlier: 5.529A pdb=" N ILE B 188 " --> pdb=" O MET B 182 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N MET B 182 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 278 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 22 through 29 removed outlier: 5.483A pdb=" N GLN C 17 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU C 2 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 101 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP C 7 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 98 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 143 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N CYS C 100 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 145 " --> pdb=" O CYS C 100 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 102 " --> pdb=" O VAL C 145 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=CC, first strand: chain 'C' and resid 187 through 194 removed outlier: 5.534A pdb=" N ILE C 188 " --> pdb=" O MET C 182 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET C 182 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 278 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 22 through 29 removed outlier: 5.496A pdb=" N GLN D 17 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU D 2 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D 101 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP D 7 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE D 98 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL D 143 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N CYS D 100 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL D 145 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 102 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=DC, first strand: chain 'D' and resid 187 through 194 removed outlier: 5.547A pdb=" N ILE D 188 " --> pdb=" O MET D 182 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET D 182 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 278 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 22 through 29 removed outlier: 5.481A pdb=" N GLN E 17 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU E 2 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR E 101 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP E 7 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE E 98 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL E 143 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS E 100 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL E 145 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU E 102 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=EC, first strand: chain 'E' and resid 187 through 194 removed outlier: 5.556A pdb=" N ILE E 188 " --> pdb=" O MET E 182 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET E 182 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 278 " --> pdb=" O PHE E 302 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1545 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: 4.14 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2456 1.32 - 1.45: 3160 1.45 - 1.57: 7164 1.57 - 1.70: 40 1.70 - 1.82: 70 Bond restraints: 12890 Sorted by residual: bond pdb=" C PHE B 4 " pdb=" N ILE B 5 " ideal model delta sigma weight residual 1.329 1.444 -0.115 1.37e-02 5.33e+03 7.07e+01 bond pdb=" N3B ANP B 500 " pdb=" PG ANP B 500 " ideal model delta sigma weight residual 1.795 1.643 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N3B ANP C 500 " pdb=" PG ANP C 500 " ideal model delta sigma weight residual 1.795 1.645 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" N3B ANP D 500 " pdb=" PG ANP D 500 " ideal model delta sigma weight residual 1.795 1.647 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N3B ANP E 500 " pdb=" PG ANP E 500 " ideal model delta sigma weight residual 1.795 1.648 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 12885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 16130 3.00 - 6.00: 1204 6.00 - 9.00: 135 9.00 - 11.99: 16 11.99 - 14.99: 10 Bond angle restraints: 17495 Sorted by residual: angle pdb=" C PHE B 4 " pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta sigma weight residual 123.11 112.68 10.43 1.36e+00 5.41e-01 5.88e+01 angle pdb=" N VAL E 66 " pdb=" CA VAL E 66 " pdb=" CB VAL E 66 " ideal model delta sigma weight residual 110.53 117.03 -6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N VAL A 66 " pdb=" CA VAL A 66 " pdb=" CB VAL A 66 " ideal model delta sigma weight residual 110.53 117.02 -6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" N VAL C 66 " pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " ideal model delta sigma weight residual 110.53 116.91 -6.38 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N VAL D 66 " pdb=" CA VAL D 66 " pdb=" CB VAL D 66 " ideal model delta sigma weight residual 110.53 116.89 -6.36 1.09e+00 8.42e-01 3.40e+01 ... (remaining 17490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 7054 30.21 - 60.41: 731 60.41 - 90.62: 65 90.62 - 120.83: 0 120.83 - 151.03: 5 Dihedral angle restraints: 7855 sinusoidal: 3230 harmonic: 4625 Sorted by residual: dihedral pdb=" CA LEU B 317 " pdb=" C LEU B 317 " pdb=" N ILE B 318 " pdb=" CA ILE B 318 " ideal model delta harmonic sigma weight residual 180.00 142.63 37.37 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA LEU A 317 " pdb=" C LEU A 317 " pdb=" N ILE A 318 " pdb=" CA ILE A 318 " ideal model delta harmonic sigma weight residual 180.00 142.75 37.25 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" CA LEU D 317 " pdb=" C LEU D 317 " pdb=" N ILE D 318 " pdb=" CA ILE D 318 " ideal model delta harmonic sigma weight residual 180.00 142.89 37.11 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 7852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1180 0.073 - 0.146: 514 0.146 - 0.219: 185 0.219 - 0.292: 84 0.292 - 0.365: 57 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ARG A 262 " pdb=" N ARG A 262 " pdb=" C ARG A 262 " pdb=" CB ARG A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASN D 268 " pdb=" N ASN D 268 " pdb=" C ASN D 268 " pdb=" CB ASN D 268 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA PHE B 46 " pdb=" N PHE B 46 " pdb=" C PHE B 46 " pdb=" CB PHE B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2017 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR E 107 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 107 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 107 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 107 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 107 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 107 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 107 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 107 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 107 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 107 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 107 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 107 " 0.042 2.00e-02 2.50e+03 2.23e-02 9.95e+00 pdb=" CG TYR D 107 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 107 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 107 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 107 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 107 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 107 " 0.018 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 839 2.74 - 3.28: 13239 3.28 - 3.82: 21743 3.82 - 4.36: 26447 4.36 - 4.90: 41415 Nonbonded interactions: 103683 Sorted by model distance: nonbonded pdb=" N ARG A 297 " pdb=" OD2 ASP C 241 " model vdw 2.197 3.120 nonbonded pdb=" N ARG C 297 " pdb=" OD2 ASP E 241 " model vdw 2.220 3.120 nonbonded pdb=" N ARG B 297 " pdb=" OD2 ASP D 241 " model vdw 2.222 3.120 nonbonded pdb=" O ASP B 164 " pdb=" N GLY B 183 " model vdw 2.303 3.120 nonbonded pdb=" O ASP E 164 " pdb=" N GLY E 183 " model vdw 2.303 3.120 ... (remaining 103678 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' } 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.770 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.152 12890 Z= 0.744 Angle : 1.714 14.993 17495 Z= 1.035 Chirality : 0.110 0.365 2020 Planarity : 0.006 0.047 2220 Dihedral : 22.055 151.032 4875 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 2.85 % Allowed : 8.67 % Favored : 88.48 % Rotamer: Outliers : 18.45 % Allowed : 22.90 % Favored : 58.66 % Cbeta Deviations : 2.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.68 % 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: -3.27 (0.18), residues: 1580 helix: -2.13 (0.17), residues: 555 sheet: -1.14 (0.26), residues: 365 loop : -2.70 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 72 HIS 0.007 0.002 HIS E 293 PHE 0.028 0.004 PHE A 138 TYR 0.047 0.007 TYR E 107 ARG 0.004 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 370 time to evaluate : 1.415 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 1 MET cc_start: 0.8575 (mpp) cc_final: 0.7635 (ttt) REVERT: A 101 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7580 (t) REVERT: A 106 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8362 (tp30) REVERT: A 107 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 111 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8560 (p0) REVERT: A 121 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8635 (mtp85) REVERT: A 148 GLU cc_start: 0.5993 (tt0) cc_final: 0.5241 (tt0) REVERT: A 158 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8447 (mm-40) REVERT: A 194 ASP cc_start: 0.7425 (t0) cc_final: 0.7049 (t0) REVERT: A 238 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8634 (mmt180) REVERT: A 261 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8263 (tp40) REVERT: A 262 ARG cc_start: 0.8642 (ptt180) cc_final: 0.8301 (ptm160) REVERT: A 292 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (ptpt) REVERT: A 302 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: A 308 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8161 (tp-100) REVERT: A 315 MET cc_start: 0.8961 (mtp) cc_final: 0.8732 (mtm) REVERT: B 1 MET cc_start: 0.8708 (mpp) cc_final: 0.8105 (ttt) REVERT: B 54 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: B 101 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.6890 (t) REVERT: B 106 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8125 (tp30) REVERT: B 107 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: B 111 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8429 (p0) REVERT: B 125 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7358 (t0) REVERT: B 148 GLU cc_start: 0.5037 (tt0) cc_final: 0.4498 (tt0) REVERT: B 194 ASP cc_start: 0.7018 (t0) cc_final: 0.6723 (t0) REVERT: B 208 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7958 (t70) REVERT: B 234 TYR cc_start: 0.9070 (t80) cc_final: 0.8284 (t80) REVERT: B 261 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8264 (tp-100) REVERT: B 292 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8209 (ptpt) REVERT: B 302 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: B 316 TYR cc_start: 0.8488 (t80) cc_final: 0.8189 (t80) REVERT: C 1 MET cc_start: 0.8735 (mpp) cc_final: 0.8212 (ttt) REVERT: C 31 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7660 (t) REVERT: C 74 TYR cc_start: 0.8150 (m-80) cc_final: 0.7668 (m-80) REVERT: C 97 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: C 101 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7049 (t) REVERT: C 106 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8002 (tp30) REVERT: C 107 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: C 111 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8218 (p0) REVERT: C 139 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.6874 (p) REVERT: C 140 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8222 (pt) REVERT: C 148 GLU cc_start: 0.5864 (tt0) cc_final: 0.5350 (tt0) REVERT: C 194 ASP cc_start: 0.7218 (t0) cc_final: 0.6911 (t70) REVERT: C 219 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 234 TYR cc_start: 0.8973 (t80) cc_final: 0.8667 (t80) REVERT: C 247 ILE cc_start: 0.8692 (tt) cc_final: 0.8435 (tt) REVERT: C 262 ARG cc_start: 0.8758 (ptt180) cc_final: 0.8490 (mtm-85) REVERT: C 292 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8151 (pttt) REVERT: D 1 MET cc_start: 0.8758 (mpp) cc_final: 0.8316 (ttt) REVERT: D 31 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (t) REVERT: D 53 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: D 74 TYR cc_start: 0.7967 (m-80) cc_final: 0.7452 (m-80) REVERT: D 101 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7122 (t) REVERT: D 106 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8223 (tp30) REVERT: D 121 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8300 (mtp85) REVERT: D 125 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7555 (t0) REVERT: D 148 GLU cc_start: 0.5630 (tt0) cc_final: 0.4961 (tt0) REVERT: D 158 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (mm-40) REVERT: D 216 LYS cc_start: 0.9041 (ttmp) cc_final: 0.8786 (tttp) REVERT: D 261 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8600 (tp40) REVERT: D 292 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8277 (mmtm) REVERT: D 310 ASP cc_start: 0.8549 (m-30) cc_final: 0.8253 (m-30) REVERT: E 1 MET cc_start: 0.8977 (mpp) cc_final: 0.8545 (ttt) REVERT: E 31 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7155 (t) REVERT: E 40 PHE cc_start: 0.7398 (t80) cc_final: 0.7087 (t80) REVERT: E 54 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6499 (pp30) REVERT: E 106 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8276 (tp30) REVERT: E 110 ARG cc_start: 0.7393 (mmp80) cc_final: 0.7101 (ttt180) REVERT: E 121 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8053 (mtp85) REVERT: E 158 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (mm-40) REVERT: E 247 ILE cc_start: 0.8774 (tt) cc_final: 0.8531 (tp) REVERT: E 261 GLN cc_start: 0.9309 (tp-100) cc_final: 0.8711 (tp40) REVERT: E 262 ARG cc_start: 0.8780 (ptt180) cc_final: 0.8469 (mtt180) REVERT: E 296 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6700 (mp) REVERT: E 302 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7738 (m-80) outliers start: 261 outliers final: 78 residues processed: 576 average time/residue: 0.2950 time to fit residues: 230.4030 Evaluate side-chains 345 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 231 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS A 118 ASN A 261 GLN A 308 GLN B 83 HIS B 261 GLN B 308 GLN C 83 HIS C 118 ASN C 308 GLN D 83 HIS D 118 ASN D 261 GLN D 308 GLN E 83 HIS E 115 ASN E 118 ASN E 125 ASN E 261 GLN E 308 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12890 Z= 0.264 Angle : 0.812 8.094 17495 Z= 0.424 Chirality : 0.047 0.203 2020 Planarity : 0.005 0.072 2220 Dihedral : 13.580 168.401 1860 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.30 % Favored : 89.94 % Rotamer: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.81 (0.19), residues: 1580 helix: -0.69 (0.20), residues: 595 sheet: -0.27 (0.27), residues: 355 loop : -2.18 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 72 HIS 0.006 0.001 HIS C 275 PHE 0.023 0.002 PHE A 4 TYR 0.027 0.002 TYR B 107 ARG 0.008 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8176 (m-80) cc_final: 0.7493 (m-10) REVERT: A 106 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 148 GLU cc_start: 0.5971 (tt0) cc_final: 0.5488 (tt0) REVERT: A 158 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8173 (mm110) REVERT: A 176 LEU cc_start: 0.8644 (tt) cc_final: 0.7835 (tt) REVERT: A 194 ASP cc_start: 0.7123 (t0) cc_final: 0.6493 (p0) REVERT: A 208 ASP cc_start: 0.8312 (m-30) cc_final: 0.7832 (p0) REVERT: A 234 TYR cc_start: 0.8733 (t80) cc_final: 0.8452 (t80) REVERT: A 244 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8664 (ttpt) REVERT: B 1 MET cc_start: 0.9045 (mpp) cc_final: 0.8368 (ttt) REVERT: B 16 TRP cc_start: 0.8723 (p-90) cc_final: 0.8054 (p90) REVERT: B 24 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8872 (mtpp) REVERT: B 74 TYR cc_start: 0.7850 (m-80) cc_final: 0.7409 (m-10) REVERT: B 126 PHE cc_start: 0.7552 (m-10) cc_final: 0.7299 (m-80) REVERT: B 142 ASP cc_start: 0.9111 (t70) cc_final: 0.8759 (t0) REVERT: B 148 GLU cc_start: 0.5230 (tt0) cc_final: 0.4909 (tt0) REVERT: B 176 LEU cc_start: 0.8702 (tt) cc_final: 0.7832 (tt) REVERT: B 194 ASP cc_start: 0.6906 (t0) cc_final: 0.6416 (p0) REVERT: B 197 LEU cc_start: 0.7835 (mp) cc_final: 0.7597 (mp) REVERT: B 234 TYR cc_start: 0.9100 (t80) cc_final: 0.8328 (t80) REVERT: B 261 GLN cc_start: 0.8617 (tp40) cc_final: 0.8326 (tp-100) REVERT: B 265 ASN cc_start: 0.8254 (m110) cc_final: 0.8045 (m-40) REVERT: B 315 MET cc_start: 0.8513 (mtm) cc_final: 0.8187 (ptp) REVERT: C 1 MET cc_start: 0.8828 (mpp) cc_final: 0.8323 (ttt) REVERT: C 24 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8858 (mttp) REVERT: C 74 TYR cc_start: 0.8049 (m-80) cc_final: 0.7375 (m-10) REVERT: C 142 ASP cc_start: 0.8958 (t70) cc_final: 0.8723 (t0) REVERT: C 148 GLU cc_start: 0.4800 (tt0) cc_final: 0.4531 (pt0) REVERT: C 194 ASP cc_start: 0.7289 (t0) cc_final: 0.6724 (p0) REVERT: C 208 ASP cc_start: 0.8129 (t70) cc_final: 0.7881 (p0) REVERT: C 234 TYR cc_start: 0.8708 (t80) cc_final: 0.8470 (t80) REVERT: C 315 MET cc_start: 0.8542 (mtm) cc_final: 0.8233 (ptp) REVERT: D 1 MET cc_start: 0.8909 (mpp) cc_final: 0.8399 (ttt) REVERT: D 16 TRP cc_start: 0.8751 (p-90) cc_final: 0.8327 (p90) REVERT: D 58 ASP cc_start: 0.8565 (t0) cc_final: 0.8335 (t0) REVERT: D 74 TYR cc_start: 0.7995 (m-80) cc_final: 0.7676 (m-80) REVERT: D 104 LEU cc_start: 0.8755 (mt) cc_final: 0.8543 (mp) REVERT: D 142 ASP cc_start: 0.8952 (t70) cc_final: 0.8640 (t70) REVERT: D 148 GLU cc_start: 0.5166 (tt0) cc_final: 0.4780 (tt0) REVERT: D 176 LEU cc_start: 0.8513 (tt) cc_final: 0.7875 (tt) REVERT: D 194 ASP cc_start: 0.6431 (t70) cc_final: 0.5937 (p0) REVERT: D 197 LEU cc_start: 0.7946 (mp) cc_final: 0.7613 (mp) REVERT: D 208 ASP cc_start: 0.8311 (t70) cc_final: 0.8036 (p0) REVERT: D 315 MET cc_start: 0.8579 (mtm) cc_final: 0.8247 (ptp) REVERT: E 1 MET cc_start: 0.8974 (mpp) cc_final: 0.8502 (ttt) REVERT: E 106 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8090 (mm-30) REVERT: E 110 ARG cc_start: 0.7543 (mmp80) cc_final: 0.7206 (ttt180) REVERT: E 117 GLU cc_start: 0.8810 (tp30) cc_final: 0.8515 (tp30) REVERT: E 121 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7702 (mtp85) REVERT: E 148 GLU cc_start: 0.5509 (tt0) cc_final: 0.5305 (pt0) REVERT: E 176 LEU cc_start: 0.8369 (tt) cc_final: 0.7521 (tt) REVERT: E 194 ASP cc_start: 0.7263 (t0) cc_final: 0.6546 (p0) REVERT: E 208 ASP cc_start: 0.8405 (t70) cc_final: 0.8167 (p0) REVERT: E 315 MET cc_start: 0.8521 (mtm) cc_final: 0.7825 (ptp) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.2975 time to fit residues: 141.9480 Evaluate side-chains 229 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 30.0000 chunk 152 optimal weight: 40.0000 chunk 125 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12890 Z= 0.243 Angle : 0.756 8.897 17495 Z= 0.394 Chirality : 0.047 0.273 2020 Planarity : 0.005 0.106 2220 Dihedral : 13.514 176.316 1860 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.06 % Favored : 89.62 % Rotamer: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.43 (0.20), residues: 1580 helix: -0.30 (0.21), residues: 590 sheet: -0.16 (0.25), residues: 385 loop : -2.06 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 72 HIS 0.009 0.002 HIS C 275 PHE 0.013 0.002 PHE D 4 TYR 0.021 0.002 TYR E 107 ARG 0.007 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 310 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7430 (tptt) cc_final: 0.7210 (tptt) REVERT: A 148 GLU cc_start: 0.5373 (tt0) cc_final: 0.5112 (tt0) REVERT: A 194 ASP cc_start: 0.7115 (t0) cc_final: 0.6711 (p0) REVERT: A 197 LEU cc_start: 0.8485 (mp) cc_final: 0.8103 (mp) REVERT: A 208 ASP cc_start: 0.8347 (m-30) cc_final: 0.7897 (p0) REVERT: B 1 MET cc_start: 0.8967 (mpp) cc_final: 0.8373 (ttt) REVERT: B 74 TYR cc_start: 0.7551 (m-80) cc_final: 0.7322 (m-10) REVERT: B 106 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 148 GLU cc_start: 0.4230 (tt0) cc_final: 0.3904 (tt0) REVERT: B 154 TYR cc_start: 0.8423 (t80) cc_final: 0.8209 (t80) REVERT: B 208 ASP cc_start: 0.8200 (p0) cc_final: 0.7955 (t70) REVERT: B 234 TYR cc_start: 0.9043 (t80) cc_final: 0.8310 (t80) REVERT: C 1 MET cc_start: 0.8725 (mpp) cc_final: 0.8240 (ttt) REVERT: C 24 LYS cc_start: 0.9221 (mmmt) cc_final: 0.9007 (mttt) REVERT: C 74 TYR cc_start: 0.7898 (m-80) cc_final: 0.7406 (m-80) REVERT: C 118 ASN cc_start: 0.7708 (m110) cc_final: 0.7453 (m-40) REVERT: C 146 MET cc_start: 0.7369 (ttp) cc_final: 0.7166 (ptm) REVERT: C 148 GLU cc_start: 0.4179 (tt0) cc_final: 0.3939 (pt0) REVERT: C 194 ASP cc_start: 0.7167 (t0) cc_final: 0.6749 (p0) REVERT: C 315 MET cc_start: 0.8482 (mtm) cc_final: 0.8268 (mtp) REVERT: D 1 MET cc_start: 0.8830 (mpp) cc_final: 0.8390 (ttt) REVERT: D 58 ASP cc_start: 0.8529 (t0) cc_final: 0.8267 (t0) REVERT: D 74 TYR cc_start: 0.7922 (m-80) cc_final: 0.7703 (m-80) REVERT: D 194 ASP cc_start: 0.6345 (t70) cc_final: 0.6098 (p0) REVERT: D 197 LEU cc_start: 0.7952 (mp) cc_final: 0.7661 (mp) REVERT: D 208 ASP cc_start: 0.8256 (t70) cc_final: 0.8025 (p0) REVERT: D 310 ASP cc_start: 0.8190 (m-30) cc_final: 0.7983 (m-30) REVERT: D 315 MET cc_start: 0.8599 (mtm) cc_final: 0.8300 (ptm) REVERT: E 1 MET cc_start: 0.8917 (mpp) cc_final: 0.8528 (ttt) REVERT: E 106 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8093 (mm-30) REVERT: E 110 ARG cc_start: 0.7319 (mmp80) cc_final: 0.7012 (ttt180) REVERT: E 146 MET cc_start: 0.7791 (ttp) cc_final: 0.7153 (ttm) REVERT: E 194 ASP cc_start: 0.7233 (t0) cc_final: 0.6541 (p0) REVERT: E 197 LEU cc_start: 0.7999 (mt) cc_final: 0.7678 (mp) REVERT: E 315 MET cc_start: 0.8512 (mtm) cc_final: 0.8171 (mtp) outliers start: 3 outliers final: 0 residues processed: 313 average time/residue: 0.2484 time to fit residues: 110.5352 Evaluate side-chains 209 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.0980 chunk 106 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 141 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12890 Z= 0.205 Angle : 0.723 8.482 17495 Z= 0.373 Chirality : 0.045 0.211 2020 Planarity : 0.005 0.075 2220 Dihedral : 13.303 177.947 1860 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.24 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: -1.07 (0.20), residues: 1580 helix: 0.12 (0.23), residues: 535 sheet: 0.28 (0.26), residues: 355 loop : -1.93 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 72 HIS 0.006 0.001 HIS C 275 PHE 0.013 0.001 PHE D 4 TYR 0.033 0.002 TYR C 234 ARG 0.006 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8541 (t0) cc_final: 0.8123 (t0) REVERT: A 146 MET cc_start: 0.7675 (mtp) cc_final: 0.7408 (mtm) REVERT: A 194 ASP cc_start: 0.6492 (t70) cc_final: 0.6186 (p0) REVERT: A 208 ASP cc_start: 0.8339 (m-30) cc_final: 0.7914 (p0) REVERT: A 230 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7735 (pttm) REVERT: B 1 MET cc_start: 0.9030 (mpp) cc_final: 0.8397 (ttt) REVERT: B 48 TYR cc_start: 0.9095 (m-80) cc_final: 0.8668 (m-80) REVERT: B 58 ASP cc_start: 0.8549 (t0) cc_final: 0.8048 (t0) REVERT: B 106 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 146 MET cc_start: 0.6788 (mtp) cc_final: 0.6491 (ttp) REVERT: B 208 ASP cc_start: 0.8232 (p0) cc_final: 0.8004 (t70) REVERT: B 234 TYR cc_start: 0.9002 (t80) cc_final: 0.8378 (t80) REVERT: B 315 MET cc_start: 0.8292 (mtm) cc_final: 0.8071 (ptp) REVERT: C 1 MET cc_start: 0.8698 (mpp) cc_final: 0.8182 (ttt) REVERT: C 58 ASP cc_start: 0.8665 (t0) cc_final: 0.8315 (t0) REVERT: C 74 TYR cc_start: 0.7990 (m-80) cc_final: 0.7329 (m-10) REVERT: C 194 ASP cc_start: 0.7154 (t0) cc_final: 0.6667 (p0) REVERT: C 223 ASP cc_start: 0.8810 (m-30) cc_final: 0.8398 (t0) REVERT: C 227 ILE cc_start: 0.8414 (mt) cc_final: 0.8208 (mt) REVERT: C 234 TYR cc_start: 0.8619 (t80) cc_final: 0.8072 (t80) REVERT: C 315 MET cc_start: 0.8667 (mtm) cc_final: 0.8427 (mtm) REVERT: D 1 MET cc_start: 0.8808 (mpp) cc_final: 0.8358 (ttt) REVERT: D 16 TRP cc_start: 0.8813 (p-90) cc_final: 0.8542 (p90) REVERT: D 74 TYR cc_start: 0.7871 (m-80) cc_final: 0.7188 (m-80) REVERT: D 106 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8069 (mm-30) REVERT: D 148 GLU cc_start: 0.5432 (tt0) cc_final: 0.5162 (pt0) REVERT: D 176 LEU cc_start: 0.8669 (tt) cc_final: 0.8115 (tt) REVERT: D 194 ASP cc_start: 0.6301 (t70) cc_final: 0.6084 (p0) REVERT: D 208 ASP cc_start: 0.8296 (t70) cc_final: 0.8064 (p0) REVERT: D 234 TYR cc_start: 0.8635 (t80) cc_final: 0.8228 (t80) REVERT: D 315 MET cc_start: 0.8526 (mtm) cc_final: 0.8079 (ptp) REVERT: E 1 MET cc_start: 0.8921 (mpp) cc_final: 0.8545 (ttt) REVERT: E 106 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8053 (mm-30) REVERT: E 110 ARG cc_start: 0.7293 (mmp80) cc_final: 0.7008 (ttt180) REVERT: E 146 MET cc_start: 0.7793 (ttp) cc_final: 0.7530 (ptm) REVERT: E 176 LEU cc_start: 0.8651 (tt) cc_final: 0.8030 (tt) REVERT: E 185 LEU cc_start: 0.8336 (mt) cc_final: 0.8080 (mt) REVERT: E 194 ASP cc_start: 0.6781 (t70) cc_final: 0.6169 (p0) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2392 time to fit residues: 97.8662 Evaluate side-chains 204 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 127 optimal weight: 50.0000 chunk 103 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 134 optimal weight: 0.6980 chunk 37 optimal weight: 0.0770 chunk 50 optimal weight: 40.0000 overall best weight: 5.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 265 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12890 Z= 0.209 Angle : 0.713 8.564 17495 Z= 0.368 Chirality : 0.045 0.231 2020 Planarity : 0.005 0.074 2220 Dihedral : 13.139 179.353 1860 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.11 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: -1.18 (0.20), residues: 1580 helix: -0.05 (0.22), residues: 555 sheet: 0.30 (0.26), residues: 355 loop : -2.02 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 16 HIS 0.005 0.001 HIS B 26 PHE 0.014 0.001 PHE D 4 TYR 0.024 0.002 TYR C 234 ARG 0.007 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8608 (t0) cc_final: 0.8190 (t0) REVERT: A 194 ASP cc_start: 0.6488 (t70) cc_final: 0.6210 (p0) REVERT: A 208 ASP cc_start: 0.8366 (m-30) cc_final: 0.7979 (p0) REVERT: A 230 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7745 (pttm) REVERT: B 1 MET cc_start: 0.9009 (mpp) cc_final: 0.8412 (ttt) REVERT: B 48 TYR cc_start: 0.9079 (m-80) cc_final: 0.8653 (m-80) REVERT: B 58 ASP cc_start: 0.8538 (t0) cc_final: 0.8070 (t0) REVERT: B 148 GLU cc_start: 0.4436 (tt0) cc_final: 0.4130 (tt0) REVERT: B 178 ILE cc_start: 0.8745 (mm) cc_final: 0.8487 (mm) REVERT: B 234 TYR cc_start: 0.8971 (t80) cc_final: 0.8381 (t80) REVERT: C 1 MET cc_start: 0.8683 (mpp) cc_final: 0.8163 (ttt) REVERT: C 63 ASP cc_start: 0.8484 (t0) cc_final: 0.8267 (t70) REVERT: C 74 TYR cc_start: 0.7911 (m-80) cc_final: 0.7226 (m-10) REVERT: C 176 LEU cc_start: 0.8717 (tt) cc_final: 0.8022 (tt) REVERT: C 194 ASP cc_start: 0.6361 (t70) cc_final: 0.6008 (p0) REVERT: C 223 ASP cc_start: 0.8792 (m-30) cc_final: 0.8404 (t0) REVERT: D 1 MET cc_start: 0.8790 (mpp) cc_final: 0.8357 (ttt) REVERT: D 176 LEU cc_start: 0.8782 (tt) cc_final: 0.8239 (tt) REVERT: D 194 ASP cc_start: 0.6509 (t70) cc_final: 0.6242 (p0) REVERT: D 208 ASP cc_start: 0.8248 (t70) cc_final: 0.8022 (p0) REVERT: D 315 MET cc_start: 0.8490 (mtm) cc_final: 0.8047 (ptp) REVERT: E 1 MET cc_start: 0.8881 (mpp) cc_final: 0.8548 (ttt) REVERT: E 106 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8088 (mm-30) REVERT: E 110 ARG cc_start: 0.7383 (mmp80) cc_final: 0.7046 (ttt180) REVERT: E 176 LEU cc_start: 0.8637 (tt) cc_final: 0.8129 (tt) REVERT: E 185 LEU cc_start: 0.8478 (mt) cc_final: 0.8196 (mt) REVERT: E 194 ASP cc_start: 0.6471 (t70) cc_final: 0.5911 (p0) REVERT: E 197 LEU cc_start: 0.8244 (mt) cc_final: 0.7954 (mt) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2397 time to fit residues: 96.1775 Evaluate side-chains 205 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 overall best weight: 5.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 118 ASN A 158 GLN A 265 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN D 78 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12890 Z= 0.214 Angle : 0.696 8.290 17495 Z= 0.363 Chirality : 0.044 0.195 2020 Planarity : 0.006 0.113 2220 Dihedral : 12.945 177.127 1860 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.05 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -1.05 (0.20), residues: 1580 helix: -0.08 (0.21), residues: 590 sheet: 0.65 (0.27), residues: 335 loop : -2.01 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 72 HIS 0.006 0.001 HIS B 26 PHE 0.012 0.001 PHE D 4 TYR 0.021 0.002 TYR E 107 ARG 0.008 0.001 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.383 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 58 ASP cc_start: 0.8646 (t0) cc_final: 0.8239 (t0) REVERT: A 208 ASP cc_start: 0.8416 (m-30) cc_final: 0.8014 (p0) REVERT: A 230 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7726 (pttm) REVERT: B 1 MET cc_start: 0.8968 (mpp) cc_final: 0.8354 (ttt) REVERT: B 48 TYR cc_start: 0.9107 (m-80) cc_final: 0.8703 (m-80) REVERT: B 54 GLN cc_start: 0.8427 (pt0) cc_final: 0.7981 (pt0) REVERT: B 58 ASP cc_start: 0.8516 (t0) cc_final: 0.8086 (t0) REVERT: B 168 ILE cc_start: 0.8555 (mp) cc_final: 0.8173 (tp) REVERT: B 178 ILE cc_start: 0.8741 (mm) cc_final: 0.8412 (mm) REVERT: B 179 SER cc_start: 0.8598 (p) cc_final: 0.8397 (p) REVERT: B 234 TYR cc_start: 0.8970 (t80) cc_final: 0.8442 (t80) REVERT: B 252 MET cc_start: 0.7532 (tmm) cc_final: 0.6744 (tmm) REVERT: C 1 MET cc_start: 0.8734 (mpp) cc_final: 0.8202 (ttt) REVERT: C 74 TYR cc_start: 0.7790 (m-80) cc_final: 0.7328 (m-80) REVERT: C 176 LEU cc_start: 0.8722 (tt) cc_final: 0.8140 (tt) REVERT: C 194 ASP cc_start: 0.6399 (t70) cc_final: 0.6182 (p0) REVERT: D 1 MET cc_start: 0.8745 (mpp) cc_final: 0.8288 (ttt) REVERT: D 176 LEU cc_start: 0.8729 (tt) cc_final: 0.8178 (tt) REVERT: D 315 MET cc_start: 0.8485 (mtm) cc_final: 0.8213 (mtp) REVERT: E 1 MET cc_start: 0.8871 (mpp) cc_final: 0.8523 (ttt) REVERT: E 106 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8120 (mm-30) REVERT: E 110 ARG cc_start: 0.7395 (mmp80) cc_final: 0.6988 (ttt180) REVERT: E 176 LEU cc_start: 0.8670 (tt) cc_final: 0.8181 (tt) REVERT: E 185 LEU cc_start: 0.8728 (mt) cc_final: 0.8458 (mt) REVERT: E 194 ASP cc_start: 0.6526 (t70) cc_final: 0.5928 (p0) REVERT: E 197 LEU cc_start: 0.8183 (mt) cc_final: 0.7900 (mt) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2356 time to fit residues: 92.6333 Evaluate side-chains 210 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 30.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12890 Z= 0.189 Angle : 0.681 8.041 17495 Z= 0.354 Chirality : 0.044 0.212 2020 Planarity : 0.005 0.092 2220 Dihedral : 12.717 172.469 1860 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.24 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: -0.93 (0.20), residues: 1580 helix: -0.00 (0.21), residues: 590 sheet: 0.93 (0.27), residues: 315 loop : -1.96 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 72 HIS 0.005 0.001 HIS B 26 PHE 0.013 0.001 PHE D 270 TYR 0.023 0.002 TYR E 107 ARG 0.008 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8614 (t0) cc_final: 0.8256 (t0) REVERT: A 146 MET cc_start: 0.7071 (mtm) cc_final: 0.6756 (ptm) REVERT: A 208 ASP cc_start: 0.8492 (m-30) cc_final: 0.8090 (p0) REVERT: A 230 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7720 (pttm) REVERT: B 1 MET cc_start: 0.8955 (mpp) cc_final: 0.8336 (ttt) REVERT: B 34 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8762 (mtm-85) REVERT: B 48 TYR cc_start: 0.9110 (m-80) cc_final: 0.8698 (m-80) REVERT: B 54 GLN cc_start: 0.8475 (pt0) cc_final: 0.8062 (pt0) REVERT: B 58 ASP cc_start: 0.8443 (t0) cc_final: 0.7973 (t0) REVERT: B 121 ARG cc_start: 0.8087 (ptp-170) cc_final: 0.7830 (ptm160) REVERT: B 158 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7718 (mm-40) REVERT: B 168 ILE cc_start: 0.8539 (mp) cc_final: 0.8164 (tp) REVERT: B 178 ILE cc_start: 0.8741 (mm) cc_final: 0.8393 (mm) REVERT: B 229 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7833 (mtm180) REVERT: B 234 TYR cc_start: 0.9017 (t80) cc_final: 0.8533 (t80) REVERT: C 1 MET cc_start: 0.8772 (mpp) cc_final: 0.8257 (ttt) REVERT: C 58 ASP cc_start: 0.8518 (t0) cc_final: 0.8204 (t0) REVERT: C 74 TYR cc_start: 0.7901 (m-80) cc_final: 0.7335 (m-80) REVERT: C 176 LEU cc_start: 0.8678 (tt) cc_final: 0.8077 (tt) REVERT: C 315 MET cc_start: 0.8447 (ptp) cc_final: 0.8047 (ptp) REVERT: D 1 MET cc_start: 0.8729 (mpp) cc_final: 0.8253 (ttt) REVERT: D 310 ASP cc_start: 0.8378 (m-30) cc_final: 0.8177 (m-30) REVERT: D 315 MET cc_start: 0.8513 (mtm) cc_final: 0.8227 (mtp) REVERT: E 1 MET cc_start: 0.8870 (mpp) cc_final: 0.8547 (ttt) REVERT: E 106 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8082 (mm-30) REVERT: E 110 ARG cc_start: 0.7380 (mmp80) cc_final: 0.6975 (ttt180) REVERT: E 176 LEU cc_start: 0.8598 (tt) cc_final: 0.8095 (tt) REVERT: E 185 LEU cc_start: 0.8679 (mt) cc_final: 0.8464 (mt) REVERT: E 194 ASP cc_start: 0.6560 (t70) cc_final: 0.5990 (p0) REVERT: E 197 LEU cc_start: 0.8168 (mt) cc_final: 0.7868 (mt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2530 time to fit residues: 102.3447 Evaluate side-chains 209 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 50.0000 chunk 117 optimal weight: 0.0170 chunk 135 optimal weight: 6.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12890 Z= 0.205 Angle : 0.672 8.116 17495 Z= 0.350 Chirality : 0.044 0.224 2020 Planarity : 0.005 0.054 2220 Dihedral : 12.665 172.291 1860 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: -0.93 (0.20), residues: 1580 helix: 0.16 (0.22), residues: 555 sheet: 0.84 (0.28), residues: 315 loop : -1.98 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 72 HIS 0.004 0.001 HIS B 26 PHE 0.015 0.001 PHE A 138 TYR 0.025 0.002 TYR E 107 ARG 0.006 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8573 (t0) cc_final: 0.8218 (t0) REVERT: A 208 ASP cc_start: 0.8490 (m-30) cc_final: 0.8090 (p0) REVERT: A 230 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7811 (pttm) REVERT: B 1 MET cc_start: 0.8805 (mpp) cc_final: 0.8247 (ttt) REVERT: B 48 TYR cc_start: 0.9113 (m-80) cc_final: 0.8854 (m-80) REVERT: B 54 GLN cc_start: 0.8534 (pt0) cc_final: 0.8092 (pt0) REVERT: B 58 ASP cc_start: 0.8152 (t0) cc_final: 0.7748 (t0) REVERT: B 74 TYR cc_start: 0.7074 (m-10) cc_final: 0.6832 (m-10) REVERT: B 106 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 158 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7830 (mm110) REVERT: B 168 ILE cc_start: 0.8524 (mp) cc_final: 0.8180 (tp) REVERT: B 178 ILE cc_start: 0.8686 (mm) cc_final: 0.8346 (mm) REVERT: B 234 TYR cc_start: 0.9009 (t80) cc_final: 0.8532 (t80) REVERT: C 1 MET cc_start: 0.8764 (mpp) cc_final: 0.8218 (ttt) REVERT: C 58 ASP cc_start: 0.8571 (t0) cc_final: 0.8311 (t0) REVERT: C 74 TYR cc_start: 0.7939 (m-80) cc_final: 0.7320 (m-80) REVERT: C 223 ASP cc_start: 0.8829 (m-30) cc_final: 0.8450 (t0) REVERT: C 227 ILE cc_start: 0.8556 (mt) cc_final: 0.8332 (mt) REVERT: C 315 MET cc_start: 0.8348 (ptp) cc_final: 0.7959 (ptp) REVERT: D 1 MET cc_start: 0.8706 (mpp) cc_final: 0.8220 (ttt) REVERT: D 315 MET cc_start: 0.8573 (mtm) cc_final: 0.8336 (mtm) REVERT: E 1 MET cc_start: 0.8858 (mpp) cc_final: 0.8534 (ttt) REVERT: E 106 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7991 (mm-30) REVERT: E 110 ARG cc_start: 0.7403 (mmp80) cc_final: 0.6988 (ttt180) REVERT: E 176 LEU cc_start: 0.8588 (tt) cc_final: 0.8092 (tt) REVERT: E 194 ASP cc_start: 0.6688 (t70) cc_final: 0.6169 (p0) REVERT: E 197 LEU cc_start: 0.8117 (mt) cc_final: 0.7836 (mt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2146 time to fit residues: 84.1882 Evaluate side-chains 203 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 40.0000 chunk 130 optimal weight: 50.0000 chunk 139 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12890 Z= 0.220 Angle : 0.684 8.161 17495 Z= 0.359 Chirality : 0.045 0.232 2020 Planarity : 0.005 0.050 2220 Dihedral : 12.680 170.619 1860 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.56 % Favored : 90.38 % Rotamer: Outliers : 0.07 % Allowed : 0.71 % Favored : 99.22 % 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: -1.02 (0.20), residues: 1580 helix: 0.10 (0.22), residues: 555 sheet: 0.69 (0.28), residues: 315 loop : -1.99 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 72 HIS 0.005 0.001 HIS A 293 PHE 0.015 0.001 PHE D 138 TYR 0.041 0.003 TYR D 234 ARG 0.010 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7443 (mtp180) cc_final: 0.6986 (mpp80) REVERT: A 58 ASP cc_start: 0.8267 (t0) cc_final: 0.7890 (t70) REVERT: A 106 GLU cc_start: 0.8383 (mp0) cc_final: 0.8174 (mm-30) REVERT: A 208 ASP cc_start: 0.8487 (m-30) cc_final: 0.8090 (p0) REVERT: A 230 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7763 (pttm) REVERT: A 315 MET cc_start: 0.8787 (mtp) cc_final: 0.8571 (mtm) REVERT: B 1 MET cc_start: 0.8840 (mpp) cc_final: 0.8303 (ttt) REVERT: B 48 TYR cc_start: 0.9106 (m-80) cc_final: 0.8849 (m-80) REVERT: B 54 GLN cc_start: 0.8523 (pt0) cc_final: 0.8081 (pt0) REVERT: B 58 ASP cc_start: 0.8157 (t0) cc_final: 0.7706 (t0) REVERT: B 74 TYR cc_start: 0.7126 (m-10) cc_final: 0.6891 (m-10) REVERT: B 106 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8036 (mm-30) REVERT: B 158 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7839 (mm-40) REVERT: B 168 ILE cc_start: 0.8519 (mp) cc_final: 0.8187 (tp) REVERT: B 178 ILE cc_start: 0.8729 (mm) cc_final: 0.8375 (mm) REVERT: B 234 TYR cc_start: 0.9025 (t80) cc_final: 0.8545 (t80) REVERT: C 1 MET cc_start: 0.8747 (mpp) cc_final: 0.8208 (ttt) REVERT: C 58 ASP cc_start: 0.8543 (t0) cc_final: 0.8339 (t70) REVERT: C 74 TYR cc_start: 0.7976 (m-80) cc_final: 0.7454 (m-80) REVERT: C 107 TYR cc_start: 0.5984 (m-10) cc_final: 0.5739 (m-10) REVERT: C 214 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7844 (ttp80) REVERT: C 223 ASP cc_start: 0.8767 (m-30) cc_final: 0.8398 (t0) REVERT: C 227 ILE cc_start: 0.8553 (mt) cc_final: 0.8339 (mt) REVERT: C 315 MET cc_start: 0.8465 (ptp) cc_final: 0.8086 (ptp) REVERT: D 1 MET cc_start: 0.8704 (mpp) cc_final: 0.8228 (ttt) REVERT: D 146 MET cc_start: 0.7740 (mtm) cc_final: 0.7420 (ptm) REVERT: D 315 MET cc_start: 0.8520 (mtm) cc_final: 0.8244 (mtm) REVERT: E 1 MET cc_start: 0.8843 (mpp) cc_final: 0.8521 (ttt) REVERT: E 106 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8015 (mm-30) REVERT: E 110 ARG cc_start: 0.7390 (mmp80) cc_final: 0.6965 (ttt180) REVERT: E 176 LEU cc_start: 0.8576 (tt) cc_final: 0.8089 (tt) REVERT: E 194 ASP cc_start: 0.6689 (t70) cc_final: 0.6162 (p0) REVERT: E 197 LEU cc_start: 0.8002 (mt) cc_final: 0.7735 (mt) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.2358 time to fit residues: 88.3093 Evaluate side-chains 199 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 102 optimal weight: 0.0270 chunk 154 optimal weight: 30.0000 chunk 142 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 overall best weight: 4.7846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12890 Z= 0.196 Angle : 0.669 8.248 17495 Z= 0.349 Chirality : 0.044 0.258 2020 Planarity : 0.005 0.048 2220 Dihedral : 12.602 171.249 1860 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.97 (0.20), residues: 1580 helix: 0.17 (0.22), residues: 555 sheet: 0.70 (0.28), residues: 315 loop : -1.98 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 72 HIS 0.005 0.001 HIS B 26 PHE 0.014 0.001 PHE D 138 TYR 0.035 0.002 TYR D 234 ARG 0.009 0.001 ARG A 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7423 (mtp180) cc_final: 0.7043 (mtt-85) REVERT: A 58 ASP cc_start: 0.8323 (t0) cc_final: 0.7993 (t0) REVERT: A 106 GLU cc_start: 0.8421 (mp0) cc_final: 0.8203 (mm-30) REVERT: A 208 ASP cc_start: 0.8509 (m-30) cc_final: 0.8166 (p0) REVERT: A 230 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7749 (pttm) REVERT: B 1 MET cc_start: 0.8799 (mpp) cc_final: 0.8252 (ttt) REVERT: B 48 TYR cc_start: 0.9089 (m-80) cc_final: 0.8710 (m-80) REVERT: B 54 GLN cc_start: 0.8562 (pt0) cc_final: 0.8125 (pt0) REVERT: B 58 ASP cc_start: 0.8197 (t0) cc_final: 0.7974 (t70) REVERT: B 106 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 146 MET cc_start: 0.7833 (mtm) cc_final: 0.7563 (ptm) REVERT: B 158 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7869 (mm-40) REVERT: B 168 ILE cc_start: 0.8518 (mp) cc_final: 0.8170 (tp) REVERT: B 178 ILE cc_start: 0.8718 (mm) cc_final: 0.8339 (mm) REVERT: B 234 TYR cc_start: 0.8991 (t80) cc_final: 0.8564 (t80) REVERT: C 1 MET cc_start: 0.8748 (mpp) cc_final: 0.8243 (ttt) REVERT: C 74 TYR cc_start: 0.8039 (m-80) cc_final: 0.7705 (m-80) REVERT: C 107 TYR cc_start: 0.5996 (m-10) cc_final: 0.5454 (m-10) REVERT: C 168 ILE cc_start: 0.8765 (mt) cc_final: 0.8451 (tp) REVERT: C 214 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7822 (ttp80) REVERT: C 223 ASP cc_start: 0.8734 (m-30) cc_final: 0.8260 (t0) REVERT: C 227 ILE cc_start: 0.8520 (mt) cc_final: 0.8207 (mt) REVERT: D 1 MET cc_start: 0.8698 (mpp) cc_final: 0.8215 (ttt) REVERT: D 146 MET cc_start: 0.7602 (mtm) cc_final: 0.7289 (ptm) REVERT: D 315 MET cc_start: 0.8547 (mtm) cc_final: 0.8256 (mtm) REVERT: E 1 MET cc_start: 0.8853 (mpp) cc_final: 0.8507 (ttt) REVERT: E 106 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8037 (mm-30) REVERT: E 110 ARG cc_start: 0.7334 (mmp80) cc_final: 0.6917 (ttt180) REVERT: E 176 LEU cc_start: 0.8589 (tt) cc_final: 0.8091 (tt) REVERT: E 194 ASP cc_start: 0.6633 (t70) cc_final: 0.6142 (p0) REVERT: E 197 LEU cc_start: 0.7967 (mt) cc_final: 0.7732 (mt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2184 time to fit residues: 81.7781 Evaluate side-chains 198 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 0.0020 chunk 123 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 overall best weight: 6.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074738 restraints weight = 48761.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076340 restraints weight = 29392.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.077401 restraints weight = 19907.886| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12890 Z= 0.228 Angle : 0.687 8.290 17495 Z= 0.360 Chirality : 0.045 0.244 2020 Planarity : 0.005 0.046 2220 Dihedral : 12.677 170.650 1860 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.02 (0.20), residues: 1580 helix: 0.20 (0.22), residues: 560 sheet: 0.65 (0.28), residues: 315 loop : -2.08 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 72 HIS 0.005 0.001 HIS D 275 PHE 0.014 0.001 PHE D 138 TYR 0.033 0.002 TYR D 234 ARG 0.005 0.001 ARG A 297 =============================================================================== Job complete usr+sys time: 2606.89 seconds wall clock time: 47 minutes 32.29 seconds (2852.29 seconds total)