Starting phenix.real_space_refine on Wed Mar 4 23:40:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v00_20966/03_2026/6v00_20966.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v00_20966/03_2026/6v00_20966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v00_20966/03_2026/6v00_20966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v00_20966/03_2026/6v00_20966.map" model { file = "/net/cci-nas-00/data/ceres_data/6v00_20966/03_2026/6v00_20966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v00_20966/03_2026/6v00_20966.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Ca 8 9.91 5 S 88 5.16 5 C 11264 2.51 5 N 2988 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2864 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 6} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 394 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, G, J, E, H, K, F, I, L Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA E 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 residue: pdb="CA CA K 202 " occ=0.83 Time building chain proxies: 2.77, per 1000 atoms: 0.16 Number of scatterers: 17460 At special positions: 0 Unit cell: (110.21, 110.21, 125.66, 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) Ca 8 19.99 S 88 16.00 O 3112 8.00 N 2988 7.00 C 11264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 764.9 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 77.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.741A pdb=" N GLY A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.904A pdb=" N THR A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.620A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.588A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.518A pdb=" N ILE B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.695A pdb=" N MET B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 97 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 98' Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.767A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.740A pdb=" N MET B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 120 through 142 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA D 152 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR D 171 " --> pdb=" O PHE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 216 Processing helix chain 'D' and resid 223 through 237 Processing helix chain 'D' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL D 241 " --> pdb=" O MET D 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE D 335 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 363 through 366 Processing helix chain 'D' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.619A pdb=" N LYS D 393 " --> pdb=" O SER D 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 394 " --> pdb=" O THR D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 509 through 532 removed outlier: 3.589A pdb=" N THR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL D 541 " --> pdb=" O ASP D 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 22 " --> pdb=" O SER E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.519A pdb=" N ILE E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.696A pdb=" N MET E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP E 96 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 97 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN E 98 " --> pdb=" O LYS E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 98' Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 129 removed outlier: 3.768A pdb=" N ARG E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA E 129 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS E 149 " --> pdb=" O MET E 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 67 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 142 Processing helix chain 'G' and resid 143 through 145 No H-bonds generated for 'chain 'G' and resid 143 through 145' Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA G 152 " --> pdb=" O ALA G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 178 removed outlier: 3.769A pdb=" N TYR G 171 " --> pdb=" O PHE G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 223 through 237 Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 266 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE G 335 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR G 377 " --> pdb=" O SER G 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 394 removed outlier: 3.619A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 390 through 394' Processing helix chain 'G' and resid 509 through 532 removed outlier: 3.589A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 54 removed outlier: 3.519A pdb=" N ILE H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.697A pdb=" N MET H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS H 95 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP H 96 " --> pdb=" O PHE H 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY H 97 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN H 98 " --> pdb=" O LYS H 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 98' Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.768A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET H 146 " --> pdb=" O PHE H 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR I 60 " --> pdb=" O ASN I 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE I 61 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU I 67 " --> pdb=" O PHE I 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG I 81 " --> pdb=" O LEU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 99 Processing helix chain 'J' and resid 105 through 115 Processing helix chain 'J' and resid 120 through 142 Processing helix chain 'J' and resid 143 through 145 No H-bonds generated for 'chain 'J' and resid 143 through 145' Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.684A pdb=" N ALA J 152 " --> pdb=" O ALA J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 178 removed outlier: 3.768A pdb=" N TYR J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 194 removed outlier: 3.742A pdb=" N GLY J 189 " --> pdb=" O VAL J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 Processing helix chain 'J' and resid 223 through 237 Processing helix chain 'J' and resid 238 through 241 removed outlier: 3.625A pdb=" N VAL J 241 " --> pdb=" O MET J 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 242 through 244 No H-bonds generated for 'chain 'J' and resid 242 through 244' Processing helix chain 'J' and resid 245 through 258 removed outlier: 3.705A pdb=" N LEU J 250 " --> pdb=" O GLY J 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL J 254 " --> pdb=" O LEU J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 284 removed outlier: 3.837A pdb=" N THR J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 266 " --> pdb=" O LEU J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 311 removed outlier: 3.821A pdb=" N THR J 311 " --> pdb=" O VAL J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 358 removed outlier: 4.109A pdb=" N PHE J 335 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER J 338 " --> pdb=" O VAL J 334 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE J 339 " --> pdb=" O PHE J 335 " (cutoff:3.500A) Proline residue: J 343 - end of helix Processing helix chain 'J' and resid 363 through 366 Processing helix chain 'J' and resid 367 through 385 removed outlier: 3.903A pdb=" N THR J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU J 385 " --> pdb=" O CYS J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 390 through 394 removed outlier: 3.620A pdb=" N LYS J 393 " --> pdb=" O SER J 390 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE J 394 " --> pdb=" O THR J 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 390 through 394' Processing helix chain 'J' and resid 509 through 532 removed outlier: 3.588A pdb=" N THR J 513 " --> pdb=" O HIS J 509 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 564 removed outlier: 3.786A pdb=" N VAL J 541 " --> pdb=" O ASP J 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 22 removed outlier: 3.695A pdb=" N GLU K 12 " --> pdb=" O GLU K 8 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 40 removed outlier: 3.837A pdb=" N VAL K 36 " --> pdb=" O GLU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 54 removed outlier: 3.518A pdb=" N ILE K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 75 removed outlier: 3.695A pdb=" N MET K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET K 73 " --> pdb=" O PHE K 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 91 removed outlier: 3.714A pdb=" N ILE K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 98 removed outlier: 5.583A pdb=" N LYS K 95 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP K 96 " --> pdb=" O PHE K 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY K 97 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN K 98 " --> pdb=" O LYS K 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 92 through 98' Processing helix chain 'K' and resid 103 through 111 Processing helix chain 'K' and resid 118 through 129 removed outlier: 3.767A pdb=" N ARG K 127 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 149 removed outlier: 3.741A pdb=" N MET K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 81 removed outlier: 4.381A pdb=" N TYR L 60 " --> pdb=" O ASN L 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU L 67 " --> pdb=" O PHE L 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 99 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'K' and resid 100 through 102 1069 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5360 1.34 - 1.46: 3419 1.46 - 1.57: 8889 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 17820 Sorted by residual: bond pdb=" CB VAL A 310 " pdb=" CG1 VAL A 310 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.51e+00 bond pdb=" CB VAL J 310 " pdb=" CG1 VAL J 310 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.48e+00 bond pdb=" CB VAL D 310 " pdb=" CG1 VAL D 310 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CB VAL G 310 " pdb=" CG1 VAL G 310 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 17815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 22479 1.70 - 3.41: 1309 3.41 - 5.11: 200 5.11 - 6.82: 60 6.82 - 8.52: 24 Bond angle restraints: 24072 Sorted by residual: angle pdb=" C LYS K 95 " pdb=" N ASP K 96 " pdb=" CA ASP K 96 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C LYS B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C LYS E 95 " pdb=" N ASP E 96 " pdb=" CA ASP E 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C LYS H 95 " pdb=" N ASP H 96 " pdb=" CA ASP H 96 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C ARG J 243 " pdb=" N GLN J 244 " pdb=" CA GLN J 244 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 ... (remaining 24067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 9843 14.40 - 28.80: 465 28.80 - 43.20: 125 43.20 - 57.60: 15 57.60 - 72.00: 20 Dihedral angle restraints: 10468 sinusoidal: 4164 harmonic: 6304 Sorted by residual: dihedral pdb=" CA HIS J 363 " pdb=" C HIS J 363 " pdb=" N PHE J 364 " pdb=" CA PHE J 364 " ideal model delta harmonic sigma weight residual -180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA HIS A 363 " pdb=" C HIS A 363 " pdb=" N PHE A 364 " pdb=" CA PHE A 364 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA HIS G 363 " pdb=" C HIS G 363 " pdb=" N PHE G 364 " pdb=" CA PHE G 364 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 10465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1459 0.039 - 0.077: 879 0.077 - 0.116: 226 0.116 - 0.154: 106 0.154 - 0.193: 18 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ARG A 116 " pdb=" N ARG A 116 " pdb=" C ARG A 116 " pdb=" CB ARG A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ARG J 116 " pdb=" N ARG J 116 " pdb=" C ARG J 116 " pdb=" CB ARG J 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA ARG D 116 " pdb=" N ARG D 116 " pdb=" C ARG D 116 " pdb=" CB ARG D 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 2685 not shown) Planarity restraints: 3028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 332 " -0.032 2.00e-02 2.50e+03 2.30e-02 9.24e+00 pdb=" CG PHE G 332 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE G 332 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 332 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE G 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 332 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 332 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 332 " -0.032 2.00e-02 2.50e+03 2.30e-02 9.24e+00 pdb=" CG PHE D 332 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 332 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 332 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE D 332 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 332 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 332 " 0.032 2.00e-02 2.50e+03 2.29e-02 9.14e+00 pdb=" CG PHE A 332 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 332 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 332 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 332 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 332 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 332 " 0.022 2.00e-02 2.50e+03 ... (remaining 3025 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5479 2.83 - 3.35: 16710 3.35 - 3.87: 28038 3.87 - 4.38: 31098 4.38 - 4.90: 55323 Nonbonded interactions: 136648 Sorted by model distance: nonbonded pdb=" OE2 GLU A 284 " pdb=" OG1 THR A 322 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU D 284 " pdb=" OG1 THR D 322 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 322 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU J 284 " pdb=" OG1 THR J 322 " model vdw 2.315 3.040 nonbonded pdb=" O LYS A 183 " pdb=" NH2 ARG A 192 " model vdw 2.359 3.120 ... (remaining 136643 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 17820 Z= 0.309 Angle : 0.954 8.521 24072 Z= 0.545 Chirality : 0.053 0.193 2688 Planarity : 0.007 0.048 3028 Dihedral : 10.226 72.001 6412 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.14), residues: 2140 helix: -2.24 (0.09), residues: 1616 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 243 TYR 0.021 0.003 TYR G 315 PHE 0.046 0.003 PHE G 332 TRP 0.028 0.003 TRP D 305 HIS 0.013 0.002 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00736 (17820) covalent geometry : angle 0.95407 (24072) hydrogen bonds : bond 0.14874 ( 1069) hydrogen bonds : angle 5.73733 ( 3183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8401 (tp) cc_final: 0.7913 (mm) REVERT: A 507 ARG cc_start: 0.7501 (mmt-90) cc_final: 0.7100 (mpt180) REVERT: B 18 SER cc_start: 0.8995 (t) cc_final: 0.8668 (p) REVERT: B 19 LEU cc_start: 0.9032 (mp) cc_final: 0.8810 (mt) REVERT: B 70 LEU cc_start: 0.8918 (tt) cc_final: 0.8176 (mt) REVERT: B 123 ASP cc_start: 0.8390 (m-30) cc_final: 0.7878 (m-30) REVERT: C 65 MET cc_start: 0.8697 (mmt) cc_final: 0.8249 (mmt) REVERT: C 81 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7181 (mmt180) REVERT: D 191 LEU cc_start: 0.8395 (tp) cc_final: 0.7927 (mm) REVERT: D 507 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7086 (mpt180) REVERT: E 18 SER cc_start: 0.9001 (t) cc_final: 0.8675 (p) REVERT: E 70 LEU cc_start: 0.8905 (tt) cc_final: 0.8183 (mt) REVERT: E 123 ASP cc_start: 0.8392 (m-30) cc_final: 0.7842 (m-30) REVERT: F 65 MET cc_start: 0.8695 (mmt) cc_final: 0.8220 (mmt) REVERT: F 81 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7130 (mmt180) REVERT: G 191 LEU cc_start: 0.8394 (tp) cc_final: 0.7924 (mm) REVERT: G 507 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7085 (mpt180) REVERT: H 18 SER cc_start: 0.9002 (t) cc_final: 0.8677 (p) REVERT: H 70 LEU cc_start: 0.8905 (tt) cc_final: 0.8182 (mt) REVERT: H 123 ASP cc_start: 0.8391 (m-30) cc_final: 0.7842 (m-30) REVERT: I 81 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7058 (mmt180) REVERT: J 191 LEU cc_start: 0.8392 (tp) cc_final: 0.7914 (mm) REVERT: J 507 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.7066 (mpt180) REVERT: K 18 SER cc_start: 0.9004 (t) cc_final: 0.8664 (p) REVERT: K 19 LEU cc_start: 0.9009 (mp) cc_final: 0.8798 (mt) REVERT: K 123 ASP cc_start: 0.8391 (m-30) cc_final: 0.7873 (m-30) REVERT: L 81 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7089 (mmt180) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.1856 time to fit residues: 120.9108 Evaluate side-chains 304 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A 386 ASN A 560 GLN B 54 ASN C 93 HIS D 376 GLN D 386 ASN D 560 GLN E 54 ASN F 93 HIS G 376 GLN G 386 ASN G 560 GLN H 54 ASN I 93 HIS J 376 GLN J 386 ASN J 560 GLN K 50 GLN K 54 ASN L 93 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100475 restraints weight = 24068.627| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.42 r_work: 0.3145 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17820 Z= 0.124 Angle : 0.519 6.013 24072 Z= 0.282 Chirality : 0.038 0.128 2688 Planarity : 0.004 0.031 3028 Dihedral : 4.501 23.408 2396 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.69 % Allowed : 8.08 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2140 helix: -0.29 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 127 TYR 0.014 0.001 TYR D 545 PHE 0.021 0.001 PHE K 17 TRP 0.015 0.002 TRP A 379 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00266 (17820) covalent geometry : angle 0.51856 (24072) hydrogen bonds : bond 0.04520 ( 1069) hydrogen bonds : angle 3.55158 ( 3183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 316 time to evaluate : 0.679 Fit side-chains REVERT: A 146 GLU cc_start: 0.8473 (tp30) cc_final: 0.8249 (tp30) REVERT: A 158 TRP cc_start: 0.7128 (m-90) cc_final: 0.6325 (m100) REVERT: A 191 LEU cc_start: 0.8173 (tp) cc_final: 0.7615 (mm) REVERT: A 286 ASP cc_start: 0.8710 (t0) cc_final: 0.8316 (t0) REVERT: A 507 ARG cc_start: 0.7841 (mmt-90) cc_final: 0.7132 (mpt180) REVERT: A 562 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7353 (ttp80) REVERT: B 22 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7344 (mttp) REVERT: B 73 MET cc_start: 0.8876 (mmm) cc_final: 0.8648 (mmm) REVERT: C 65 MET cc_start: 0.8796 (mmt) cc_final: 0.8502 (mmt) REVERT: C 81 ARG cc_start: 0.7683 (mtp180) cc_final: 0.6825 (mpt180) REVERT: D 146 GLU cc_start: 0.8455 (tp30) cc_final: 0.8236 (tp30) REVERT: D 158 TRP cc_start: 0.7110 (m-90) cc_final: 0.6300 (m100) REVERT: D 191 LEU cc_start: 0.8130 (tp) cc_final: 0.7574 (mm) REVERT: D 286 ASP cc_start: 0.8690 (t0) cc_final: 0.8298 (t0) REVERT: D 507 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7115 (mpt180) REVERT: D 562 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7327 (ttp80) REVERT: E 22 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7366 (mttp) REVERT: E 73 MET cc_start: 0.8878 (mmm) cc_final: 0.8643 (mmm) REVERT: F 65 MET cc_start: 0.8820 (mmt) cc_final: 0.8558 (mmt) REVERT: F 81 ARG cc_start: 0.7675 (mtp180) cc_final: 0.6944 (mpt180) REVERT: G 146 GLU cc_start: 0.8438 (tp30) cc_final: 0.8219 (tp30) REVERT: G 158 TRP cc_start: 0.7114 (m-90) cc_final: 0.6304 (m100) REVERT: G 191 LEU cc_start: 0.8130 (tp) cc_final: 0.7577 (mm) REVERT: G 286 ASP cc_start: 0.8681 (t0) cc_final: 0.8288 (t0) REVERT: G 507 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7115 (mpt180) REVERT: G 562 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7329 (ttp80) REVERT: H 22 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7312 (mttp) REVERT: H 73 MET cc_start: 0.8875 (mmm) cc_final: 0.8641 (mmm) REVERT: I 65 MET cc_start: 0.8811 (mmt) cc_final: 0.8422 (mmt) REVERT: I 81 ARG cc_start: 0.7714 (mtp180) cc_final: 0.6822 (mpt180) REVERT: J 146 GLU cc_start: 0.8439 (tp30) cc_final: 0.8224 (tp30) REVERT: J 158 TRP cc_start: 0.7116 (m-90) cc_final: 0.6314 (m100) REVERT: J 191 LEU cc_start: 0.8113 (tp) cc_final: 0.7560 (mm) REVERT: J 286 ASP cc_start: 0.8685 (t0) cc_final: 0.8294 (t0) REVERT: J 507 ARG cc_start: 0.7860 (mmt-90) cc_final: 0.7118 (mpt180) REVERT: J 562 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7330 (ttp80) REVERT: K 18 SER cc_start: 0.8891 (t) cc_final: 0.8510 (p) REVERT: K 22 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7372 (mttp) REVERT: K 73 MET cc_start: 0.8885 (mmm) cc_final: 0.8656 (mmm) REVERT: L 65 MET cc_start: 0.8844 (mmt) cc_final: 0.8477 (mmt) REVERT: L 81 ARG cc_start: 0.7647 (mtp180) cc_final: 0.6810 (mpt180) outliers start: 31 outliers final: 26 residues processed: 339 average time/residue: 0.1823 time to fit residues: 84.1731 Evaluate side-chains 282 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 145 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 0.0370 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS B 144 GLN D 510 HIS E 54 ASN E 144 GLN G 510 HIS H 54 ASN H 144 GLN J 510 HIS K 144 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.134689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101085 restraints weight = 24137.893| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.54 r_work: 0.3144 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17820 Z= 0.123 Angle : 0.476 5.957 24072 Z= 0.256 Chirality : 0.038 0.134 2688 Planarity : 0.003 0.025 3028 Dihedral : 4.034 20.026 2396 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.24 % Allowed : 9.28 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2140 helix: 0.65 (0.12), residues: 1624 sheet: None (None), residues: 0 loop : -0.88 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 127 TYR 0.014 0.001 TYR J 545 PHE 0.018 0.001 PHE A 332 TRP 0.012 0.001 TRP A 379 HIS 0.005 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00280 (17820) covalent geometry : angle 0.47640 (24072) hydrogen bonds : bond 0.03999 ( 1069) hydrogen bonds : angle 3.20380 ( 3183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8418 (tp30) cc_final: 0.8152 (tp30) REVERT: A 158 TRP cc_start: 0.7134 (m-90) cc_final: 0.6357 (m100) REVERT: A 188 TRP cc_start: 0.8390 (m100) cc_final: 0.8062 (m-90) REVERT: A 191 LEU cc_start: 0.8152 (tp) cc_final: 0.7552 (mm) REVERT: A 286 ASP cc_start: 0.8694 (t0) cc_final: 0.8228 (t0) REVERT: A 366 ARG cc_start: 0.9224 (tpp-160) cc_final: 0.9015 (tpp80) REVERT: A 507 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7111 (mpt180) REVERT: A 562 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7550 (ttp80) REVERT: B 18 SER cc_start: 0.8858 (t) cc_final: 0.8522 (p) REVERT: B 22 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7241 (mttp) REVERT: B 73 MET cc_start: 0.8833 (mmm) cc_final: 0.8570 (mmm) REVERT: C 59 MET cc_start: 0.8476 (mtt) cc_final: 0.8269 (mtt) REVERT: C 65 MET cc_start: 0.8775 (mmt) cc_final: 0.8459 (mmt) REVERT: C 81 ARG cc_start: 0.7609 (mtp180) cc_final: 0.6966 (ttp-170) REVERT: D 146 GLU cc_start: 0.8399 (tp30) cc_final: 0.8128 (tp30) REVERT: D 158 TRP cc_start: 0.7055 (m-90) cc_final: 0.6301 (m100) REVERT: D 188 TRP cc_start: 0.8408 (m100) cc_final: 0.8070 (m-90) REVERT: D 191 LEU cc_start: 0.8130 (tp) cc_final: 0.7530 (mm) REVERT: D 286 ASP cc_start: 0.8693 (t0) cc_final: 0.8241 (t0) REVERT: D 366 ARG cc_start: 0.9225 (tpp-160) cc_final: 0.9017 (tpp80) REVERT: D 507 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7136 (mpt180) REVERT: D 562 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7526 (ttp80) REVERT: E 18 SER cc_start: 0.8864 (t) cc_final: 0.8526 (p) REVERT: E 73 MET cc_start: 0.8834 (mmm) cc_final: 0.8543 (mmm) REVERT: F 65 MET cc_start: 0.8787 (mmt) cc_final: 0.8445 (mmt) REVERT: F 81 ARG cc_start: 0.7573 (mtp180) cc_final: 0.6892 (ttp-170) REVERT: G 146 GLU cc_start: 0.8392 (tp30) cc_final: 0.8124 (tp30) REVERT: G 158 TRP cc_start: 0.7053 (m-90) cc_final: 0.6302 (m100) REVERT: G 188 TRP cc_start: 0.8408 (m100) cc_final: 0.8070 (m-90) REVERT: G 191 LEU cc_start: 0.8129 (tp) cc_final: 0.7531 (mm) REVERT: G 286 ASP cc_start: 0.8676 (t0) cc_final: 0.8225 (t0) REVERT: G 366 ARG cc_start: 0.9226 (tpp-160) cc_final: 0.9021 (tpp80) REVERT: G 507 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7137 (mpt180) REVERT: G 562 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7515 (ttp80) REVERT: H 18 SER cc_start: 0.8855 (t) cc_final: 0.8519 (p) REVERT: H 54 ASN cc_start: 0.8517 (m110) cc_final: 0.8127 (m-40) REVERT: H 73 MET cc_start: 0.8835 (mmm) cc_final: 0.8544 (mmm) REVERT: I 65 MET cc_start: 0.8790 (mmt) cc_final: 0.8412 (mmt) REVERT: I 81 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6922 (ttp-170) REVERT: J 146 GLU cc_start: 0.8397 (tp30) cc_final: 0.8132 (tp30) REVERT: J 158 TRP cc_start: 0.7124 (m-90) cc_final: 0.6354 (m100) REVERT: J 188 TRP cc_start: 0.8399 (m100) cc_final: 0.8066 (m-90) REVERT: J 191 LEU cc_start: 0.8142 (tp) cc_final: 0.7551 (mm) REVERT: J 286 ASP cc_start: 0.8672 (t0) cc_final: 0.8218 (t0) REVERT: J 366 ARG cc_start: 0.9227 (tpp-160) cc_final: 0.9010 (tpp80) REVERT: J 507 ARG cc_start: 0.7903 (mmt-90) cc_final: 0.7111 (mpt180) REVERT: J 562 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7523 (ttp80) REVERT: K 18 SER cc_start: 0.8840 (t) cc_final: 0.8496 (p) REVERT: K 70 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8079 (mt) REVERT: K 73 MET cc_start: 0.8799 (mmm) cc_final: 0.8497 (mmm) REVERT: L 59 MET cc_start: 0.8491 (mtt) cc_final: 0.8264 (mtt) REVERT: L 65 MET cc_start: 0.8798 (mmt) cc_final: 0.8442 (mmt) REVERT: L 81 ARG cc_start: 0.7548 (mtp180) cc_final: 0.6920 (ttp-170) outliers start: 41 outliers final: 28 residues processed: 314 average time/residue: 0.1677 time to fit residues: 73.3085 Evaluate side-chains 296 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 332 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 39 optimal weight: 0.0000 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN E 54 ASN F 98 ASN K 50 GLN K 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100930 restraints weight = 24338.619| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.36 r_work: 0.3104 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17820 Z= 0.145 Angle : 0.481 5.801 24072 Z= 0.259 Chirality : 0.039 0.135 2688 Planarity : 0.003 0.026 3028 Dihedral : 3.880 17.525 2396 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.84 % Allowed : 9.72 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2140 helix: 1.15 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -0.77 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 127 TYR 0.017 0.001 TYR A 545 PHE 0.017 0.001 PHE A 332 TRP 0.013 0.001 TRP A 379 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00344 (17820) covalent geometry : angle 0.48073 (24072) hydrogen bonds : bond 0.04105 ( 1069) hydrogen bonds : angle 3.17843 ( 3183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 279 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7198 (m-90) cc_final: 0.6464 (m100) REVERT: A 188 TRP cc_start: 0.8463 (m100) cc_final: 0.8106 (m-90) REVERT: A 286 ASP cc_start: 0.8918 (t0) cc_final: 0.8452 (t0) REVERT: A 366 ARG cc_start: 0.9252 (tpp-160) cc_final: 0.9021 (tpp80) REVERT: A 562 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7707 (ttp80) REVERT: B 18 SER cc_start: 0.8870 (t) cc_final: 0.8557 (p) REVERT: B 46 GLU cc_start: 0.7804 (tp30) cc_final: 0.7583 (tp30) REVERT: B 54 ASN cc_start: 0.8663 (m110) cc_final: 0.8305 (m-40) REVERT: C 65 MET cc_start: 0.8804 (mmt) cc_final: 0.8391 (mmt) REVERT: C 81 ARG cc_start: 0.7658 (mtp180) cc_final: 0.6929 (ttp-170) REVERT: D 158 TRP cc_start: 0.7191 (m-90) cc_final: 0.6456 (m100) REVERT: D 188 TRP cc_start: 0.8462 (m100) cc_final: 0.8102 (m-90) REVERT: D 234 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8132 (mt0) REVERT: D 286 ASP cc_start: 0.8898 (t0) cc_final: 0.8436 (t0) REVERT: D 366 ARG cc_start: 0.9244 (tpp-160) cc_final: 0.8982 (tpp80) REVERT: D 562 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7693 (ttp80) REVERT: E 18 SER cc_start: 0.8867 (t) cc_final: 0.8546 (p) REVERT: E 22 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7332 (mttp) REVERT: E 46 GLU cc_start: 0.7808 (tp30) cc_final: 0.7590 (tp30) REVERT: E 54 ASN cc_start: 0.8685 (m110) cc_final: 0.8364 (m-40) REVERT: F 65 MET cc_start: 0.8825 (mmt) cc_final: 0.8449 (mmt) REVERT: F 81 ARG cc_start: 0.7677 (mtp180) cc_final: 0.6814 (ttp-170) REVERT: G 158 TRP cc_start: 0.7190 (m-90) cc_final: 0.6457 (m100) REVERT: G 188 TRP cc_start: 0.8466 (m100) cc_final: 0.8104 (m-90) REVERT: G 234 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8138 (mt0) REVERT: G 286 ASP cc_start: 0.8907 (t0) cc_final: 0.8444 (t0) REVERT: G 366 ARG cc_start: 0.9250 (tpp-160) cc_final: 0.8986 (tpp80) REVERT: G 562 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7692 (ttp80) REVERT: H 18 SER cc_start: 0.8863 (t) cc_final: 0.8545 (p) REVERT: H 22 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7339 (mttp) REVERT: H 46 GLU cc_start: 0.7812 (tp30) cc_final: 0.7578 (tp30) REVERT: H 54 ASN cc_start: 0.8608 (m110) cc_final: 0.8351 (m-40) REVERT: I 65 MET cc_start: 0.8813 (mmt) cc_final: 0.8409 (mmt) REVERT: I 81 ARG cc_start: 0.7641 (mtp180) cc_final: 0.6476 (mmt180) REVERT: J 158 TRP cc_start: 0.7188 (m-90) cc_final: 0.6455 (m100) REVERT: J 188 TRP cc_start: 0.8453 (m100) cc_final: 0.8096 (m-90) REVERT: J 234 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8134 (mt0) REVERT: J 286 ASP cc_start: 0.8911 (t0) cc_final: 0.8448 (t0) REVERT: J 366 ARG cc_start: 0.9244 (tpp-160) cc_final: 0.9010 (tpp80) REVERT: J 562 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7696 (ttp80) REVERT: K 18 SER cc_start: 0.8870 (t) cc_final: 0.8548 (p) REVERT: K 22 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7349 (mttp) REVERT: K 38 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8412 (mtm-85) REVERT: K 54 ASN cc_start: 0.8632 (m110) cc_final: 0.8249 (m-40) REVERT: L 65 MET cc_start: 0.8823 (mmt) cc_final: 0.8426 (mmt) REVERT: L 81 ARG cc_start: 0.7646 (mtp180) cc_final: 0.6891 (ttp-170) outliers start: 52 outliers final: 32 residues processed: 313 average time/residue: 0.1618 time to fit residues: 71.5681 Evaluate side-chains 295 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 514 ILE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN E 144 GLN F 56 ASN H 144 GLN K 144 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098469 restraints weight = 24092.054| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.39 r_work: 0.3121 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17820 Z= 0.119 Angle : 0.454 5.657 24072 Z= 0.243 Chirality : 0.038 0.125 2688 Planarity : 0.003 0.031 3028 Dihedral : 3.702 15.587 2396 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.51 % Allowed : 11.46 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.18), residues: 2140 helix: 1.54 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 127 TYR 0.013 0.001 TYR D 545 PHE 0.015 0.001 PHE J 332 TRP 0.012 0.001 TRP A 379 HIS 0.005 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00276 (17820) covalent geometry : angle 0.45449 (24072) hydrogen bonds : bond 0.03764 ( 1069) hydrogen bonds : angle 3.04121 ( 3183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7138 (m-90) cc_final: 0.6391 (m100) REVERT: A 286 ASP cc_start: 0.8942 (t0) cc_final: 0.8445 (t0) REVERT: A 366 ARG cc_start: 0.9232 (tpp-160) cc_final: 0.8982 (tpp80) REVERT: A 562 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7768 (ttp80) REVERT: B 18 SER cc_start: 0.8929 (t) cc_final: 0.8633 (p) REVERT: B 22 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7241 (mttp) REVERT: B 38 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8338 (mtm110) REVERT: B 46 GLU cc_start: 0.7761 (tp30) cc_final: 0.7534 (tp30) REVERT: B 54 ASN cc_start: 0.8638 (m110) cc_final: 0.8398 (m-40) REVERT: C 65 MET cc_start: 0.8792 (mmt) cc_final: 0.8403 (mmt) REVERT: C 81 ARG cc_start: 0.7556 (mtp180) cc_final: 0.6845 (ttp-170) REVERT: D 158 TRP cc_start: 0.7151 (m-90) cc_final: 0.6405 (m100) REVERT: D 286 ASP cc_start: 0.8933 (t0) cc_final: 0.8440 (t0) REVERT: D 366 ARG cc_start: 0.9228 (tpp-160) cc_final: 0.9012 (tpp80) REVERT: D 562 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7836 (ttp80) REVERT: E 18 SER cc_start: 0.8921 (t) cc_final: 0.8621 (p) REVERT: E 22 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7297 (mttp) REVERT: E 38 ARG cc_start: 0.8697 (mtm110) cc_final: 0.8333 (mtm110) REVERT: E 54 ASN cc_start: 0.8590 (m110) cc_final: 0.8383 (m-40) REVERT: F 65 MET cc_start: 0.8804 (mmt) cc_final: 0.8445 (mmt) REVERT: F 81 ARG cc_start: 0.7628 (mtp180) cc_final: 0.6855 (ttp-170) REVERT: G 158 TRP cc_start: 0.7152 (m-90) cc_final: 0.6407 (m100) REVERT: G 286 ASP cc_start: 0.8937 (t0) cc_final: 0.8444 (t0) REVERT: G 366 ARG cc_start: 0.9226 (tpp-160) cc_final: 0.9011 (tpp80) REVERT: G 562 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7840 (ttp80) REVERT: H 18 SER cc_start: 0.8917 (t) cc_final: 0.8619 (p) REVERT: H 22 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7304 (mttp) REVERT: H 38 ARG cc_start: 0.8703 (mtm110) cc_final: 0.8339 (mtm110) REVERT: H 46 GLU cc_start: 0.7773 (tp30) cc_final: 0.7543 (tp30) REVERT: H 54 ASN cc_start: 0.8589 (m110) cc_final: 0.8356 (m-40) REVERT: I 65 MET cc_start: 0.8798 (mmt) cc_final: 0.8410 (mmt) REVERT: I 81 ARG cc_start: 0.7556 (mtp180) cc_final: 0.6766 (ttp-170) REVERT: J 158 TRP cc_start: 0.7141 (m-90) cc_final: 0.6403 (m100) REVERT: J 286 ASP cc_start: 0.8945 (t0) cc_final: 0.8452 (t0) REVERT: J 366 ARG cc_start: 0.9223 (tpp-160) cc_final: 0.8966 (tpp80) REVERT: J 562 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7842 (ttp80) REVERT: K 18 SER cc_start: 0.8894 (t) cc_final: 0.8599 (p) REVERT: K 22 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7323 (mttp) REVERT: K 38 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8379 (mtm-85) REVERT: K 54 ASN cc_start: 0.8616 (m110) cc_final: 0.8389 (m-40) REVERT: L 65 MET cc_start: 0.8801 (mmt) cc_final: 0.8410 (mmt) REVERT: L 81 ARG cc_start: 0.7578 (mtp180) cc_final: 0.6754 (ttp-170) outliers start: 46 outliers final: 24 residues processed: 318 average time/residue: 0.1696 time to fit residues: 74.6225 Evaluate side-chains 284 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 185 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098913 restraints weight = 24052.344| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.38 r_work: 0.3128 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17820 Z= 0.114 Angle : 0.449 5.865 24072 Z= 0.241 Chirality : 0.037 0.123 2688 Planarity : 0.003 0.032 3028 Dihedral : 3.572 13.715 2396 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.67 % Allowed : 11.68 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.18), residues: 2140 helix: 1.74 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.51 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 127 TYR 0.012 0.001 TYR A 545 PHE 0.016 0.001 PHE D 332 TRP 0.011 0.001 TRP D 379 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00259 (17820) covalent geometry : angle 0.44927 (24072) hydrogen bonds : bond 0.03649 ( 1069) hydrogen bonds : angle 2.97259 ( 3183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7120 (m-90) cc_final: 0.6426 (m100) REVERT: A 286 ASP cc_start: 0.8904 (t0) cc_final: 0.8377 (t0) REVERT: A 366 ARG cc_start: 0.9202 (tpp-160) cc_final: 0.8950 (tpp80) REVERT: A 562 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7871 (ttp80) REVERT: B 22 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7320 (mttp) REVERT: B 54 ASN cc_start: 0.8696 (m110) cc_final: 0.8402 (m-40) REVERT: C 65 MET cc_start: 0.8801 (mmt) cc_final: 0.8420 (mmt) REVERT: C 81 ARG cc_start: 0.7561 (mtp180) cc_final: 0.6834 (ttp-170) REVERT: D 146 GLU cc_start: 0.8346 (tp30) cc_final: 0.8092 (tm-30) REVERT: D 158 TRP cc_start: 0.7137 (m-90) cc_final: 0.6409 (m100) REVERT: D 286 ASP cc_start: 0.8905 (t0) cc_final: 0.8382 (t0) REVERT: D 366 ARG cc_start: 0.9249 (tpp-160) cc_final: 0.8998 (tpp80) REVERT: D 562 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7881 (ttp80) REVERT: E 22 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7310 (mttp) REVERT: E 54 ASN cc_start: 0.8664 (m110) cc_final: 0.8404 (m-40) REVERT: F 65 MET cc_start: 0.8808 (mmt) cc_final: 0.8451 (mmt) REVERT: F 81 ARG cc_start: 0.7500 (mtp180) cc_final: 0.6739 (ttp-170) REVERT: G 146 GLU cc_start: 0.8328 (tp30) cc_final: 0.8077 (tm-30) REVERT: G 158 TRP cc_start: 0.7132 (m-90) cc_final: 0.6410 (m100) REVERT: G 286 ASP cc_start: 0.8898 (t0) cc_final: 0.8374 (t0) REVERT: G 366 ARG cc_start: 0.9241 (tpp-160) cc_final: 0.8988 (tpp80) REVERT: G 562 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7877 (ttp80) REVERT: H 21 ASP cc_start: 0.7661 (t0) cc_final: 0.7459 (t0) REVERT: H 22 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7314 (mttp) REVERT: H 54 ASN cc_start: 0.8681 (m110) cc_final: 0.8384 (m-40) REVERT: I 65 MET cc_start: 0.8798 (mmt) cc_final: 0.8399 (mmt) REVERT: I 81 ARG cc_start: 0.7443 (mtp180) cc_final: 0.6723 (ttp-170) REVERT: J 158 TRP cc_start: 0.7124 (m-90) cc_final: 0.6406 (m100) REVERT: J 286 ASP cc_start: 0.8908 (t0) cc_final: 0.8383 (t0) REVERT: J 366 ARG cc_start: 0.9196 (tpp-160) cc_final: 0.8937 (tpp80) REVERT: J 562 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7875 (ttp80) REVERT: K 22 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7260 (mttp) REVERT: K 54 ASN cc_start: 0.8671 (m110) cc_final: 0.8387 (m-40) REVERT: L 65 MET cc_start: 0.8793 (mmt) cc_final: 0.8395 (mmt) REVERT: L 81 ARG cc_start: 0.7511 (mtp180) cc_final: 0.6746 (ttp-170) outliers start: 49 outliers final: 32 residues processed: 297 average time/residue: 0.1654 time to fit residues: 68.6919 Evaluate side-chains 289 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 363 HIS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 566 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain J residue 566 SER Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 203 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097992 restraints weight = 24138.252| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.37 r_work: 0.3114 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17820 Z= 0.126 Angle : 0.461 5.827 24072 Z= 0.247 Chirality : 0.038 0.122 2688 Planarity : 0.003 0.043 3028 Dihedral : 3.542 13.179 2396 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.62 % Allowed : 12.45 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.18), residues: 2140 helix: 1.73 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 127 TYR 0.014 0.001 TYR J 545 PHE 0.016 0.001 PHE D 332 TRP 0.011 0.001 TRP D 379 HIS 0.005 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00295 (17820) covalent geometry : angle 0.46072 (24072) hydrogen bonds : bond 0.03752 ( 1069) hydrogen bonds : angle 3.00123 ( 3183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7121 (m-90) cc_final: 0.6444 (m100) REVERT: A 286 ASP cc_start: 0.8947 (t0) cc_final: 0.8408 (t0) REVERT: A 366 ARG cc_start: 0.9219 (tpp-160) cc_final: 0.8975 (tpp80) REVERT: A 562 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7943 (ttp80) REVERT: B 38 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8386 (mtm110) REVERT: B 54 ASN cc_start: 0.8694 (m110) cc_final: 0.8348 (m-40) REVERT: C 65 MET cc_start: 0.8800 (mmt) cc_final: 0.8423 (mmt) REVERT: C 81 ARG cc_start: 0.7600 (mtp180) cc_final: 0.6817 (ttp-170) REVERT: D 146 GLU cc_start: 0.8287 (tp30) cc_final: 0.8049 (tm-30) REVERT: D 158 TRP cc_start: 0.7120 (m-90) cc_final: 0.6438 (m100) REVERT: D 286 ASP cc_start: 0.8954 (t0) cc_final: 0.8423 (t0) REVERT: D 366 ARG cc_start: 0.9229 (tpp-160) cc_final: 0.8977 (tpp80) REVERT: D 562 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7932 (ttp80) REVERT: E 22 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7227 (mttp) REVERT: E 38 ARG cc_start: 0.8683 (mtm110) cc_final: 0.8384 (mtm110) REVERT: F 65 MET cc_start: 0.8808 (mmt) cc_final: 0.8435 (mmt) REVERT: F 81 ARG cc_start: 0.7620 (mtp180) cc_final: 0.6810 (ttp-170) REVERT: G 146 GLU cc_start: 0.8274 (tp30) cc_final: 0.8038 (tm-30) REVERT: G 158 TRP cc_start: 0.7109 (m-90) cc_final: 0.6434 (m100) REVERT: G 286 ASP cc_start: 0.8943 (t0) cc_final: 0.8408 (t0) REVERT: G 366 ARG cc_start: 0.9241 (tpp-160) cc_final: 0.8992 (tpp80) REVERT: G 562 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7931 (ttp80) REVERT: H 22 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7313 (mttp) REVERT: H 38 ARG cc_start: 0.8689 (mtm110) cc_final: 0.8389 (mtm110) REVERT: H 54 ASN cc_start: 0.8673 (m110) cc_final: 0.8344 (m-40) REVERT: I 65 MET cc_start: 0.8803 (mmt) cc_final: 0.8437 (mmt) REVERT: I 81 ARG cc_start: 0.7567 (mtp180) cc_final: 0.6795 (ttp-170) REVERT: J 158 TRP cc_start: 0.7125 (m-90) cc_final: 0.6439 (m100) REVERT: J 242 ASP cc_start: 0.8597 (t0) cc_final: 0.8379 (t0) REVERT: J 286 ASP cc_start: 0.8956 (t0) cc_final: 0.8424 (t0) REVERT: J 366 ARG cc_start: 0.9210 (tpp-160) cc_final: 0.8964 (tpp80) REVERT: J 562 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7932 (ttp80) REVERT: K 22 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7310 (mttp) REVERT: K 38 ARG cc_start: 0.8726 (mtm110) cc_final: 0.8386 (mtm110) REVERT: L 65 MET cc_start: 0.8807 (mmt) cc_final: 0.8430 (mmt) REVERT: L 81 ARG cc_start: 0.7540 (mtp180) cc_final: 0.6736 (ttp-170) outliers start: 48 outliers final: 33 residues processed: 306 average time/residue: 0.1690 time to fit residues: 71.4746 Evaluate side-chains 299 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 363 HIS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 566 SER Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain J residue 566 SER Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 9 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098557 restraints weight = 24161.388| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.38 r_work: 0.3122 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17820 Z= 0.117 Angle : 0.464 5.994 24072 Z= 0.248 Chirality : 0.038 0.122 2688 Planarity : 0.003 0.049 3028 Dihedral : 3.500 13.501 2396 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.35 % Allowed : 13.16 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2140 helix: 1.83 (0.13), residues: 1632 sheet: None (None), residues: 0 loop : -0.45 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 127 TYR 0.012 0.001 TYR D 545 PHE 0.015 0.001 PHE D 332 TRP 0.011 0.001 TRP D 379 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00272 (17820) covalent geometry : angle 0.46356 (24072) hydrogen bonds : bond 0.03649 ( 1069) hydrogen bonds : angle 2.96980 ( 3183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7113 (m-90) cc_final: 0.6383 (m100) REVERT: A 286 ASP cc_start: 0.8948 (t0) cc_final: 0.8415 (t0) REVERT: A 366 ARG cc_start: 0.9197 (tpp-160) cc_final: 0.8964 (tpp80) REVERT: A 528 LYS cc_start: 0.8244 (mttp) cc_final: 0.7938 (mmtm) REVERT: A 562 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7948 (ttp80) REVERT: B 38 ARG cc_start: 0.8679 (mtm110) cc_final: 0.8392 (mtm110) REVERT: B 54 ASN cc_start: 0.8680 (m110) cc_final: 0.8327 (m-40) REVERT: C 65 MET cc_start: 0.8802 (mmt) cc_final: 0.8401 (mmt) REVERT: C 81 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6716 (ttp-170) REVERT: D 158 TRP cc_start: 0.7117 (m-90) cc_final: 0.6382 (m100) REVERT: D 286 ASP cc_start: 0.8972 (t0) cc_final: 0.8452 (t0) REVERT: D 366 ARG cc_start: 0.9240 (tpp-160) cc_final: 0.9003 (tpp80) REVERT: D 562 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7941 (ttp80) REVERT: E 38 ARG cc_start: 0.8679 (mtm110) cc_final: 0.8392 (mtm110) REVERT: F 65 MET cc_start: 0.8805 (mmt) cc_final: 0.8422 (mmt) REVERT: F 81 ARG cc_start: 0.7622 (mtp180) cc_final: 0.6794 (ttp-170) REVERT: G 146 GLU cc_start: 0.8242 (tp30) cc_final: 0.8017 (tm-30) REVERT: G 158 TRP cc_start: 0.7105 (m-90) cc_final: 0.6381 (m100) REVERT: G 286 ASP cc_start: 0.8961 (t0) cc_final: 0.8437 (t0) REVERT: G 366 ARG cc_start: 0.9249 (tpp-160) cc_final: 0.9010 (tpp80) REVERT: G 562 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7941 (ttp80) REVERT: H 22 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7219 (mttp) REVERT: H 38 ARG cc_start: 0.8681 (mtm110) cc_final: 0.8394 (mtm110) REVERT: H 54 ASN cc_start: 0.8642 (m110) cc_final: 0.8290 (m-40) REVERT: I 65 MET cc_start: 0.8804 (mmt) cc_final: 0.8413 (mmt) REVERT: I 81 ARG cc_start: 0.7495 (mtp180) cc_final: 0.6705 (ttp-170) REVERT: J 158 TRP cc_start: 0.7092 (m-90) cc_final: 0.6369 (m100) REVERT: J 242 ASP cc_start: 0.8601 (t0) cc_final: 0.8379 (t0) REVERT: J 286 ASP cc_start: 0.8973 (t0) cc_final: 0.8448 (t0) REVERT: J 366 ARG cc_start: 0.9186 (tpp-160) cc_final: 0.8951 (tpp80) REVERT: J 528 LYS cc_start: 0.8212 (mttp) cc_final: 0.7917 (mmtm) REVERT: J 562 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7935 (ttp80) REVERT: K 22 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7247 (mttp) REVERT: L 65 MET cc_start: 0.8793 (mmt) cc_final: 0.8403 (mmt) REVERT: L 81 ARG cc_start: 0.7523 (mtp180) cc_final: 0.6732 (ttp-170) outliers start: 43 outliers final: 31 residues processed: 303 average time/residue: 0.1701 time to fit residues: 71.2569 Evaluate side-chains 300 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 363 HIS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 164 optimal weight: 0.0670 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN I 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095159 restraints weight = 24533.147| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.38 r_work: 0.3072 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17820 Z= 0.167 Angle : 0.515 5.924 24072 Z= 0.275 Chirality : 0.040 0.131 2688 Planarity : 0.003 0.053 3028 Dihedral : 3.644 13.742 2396 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.02 % Allowed : 13.81 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2140 helix: 1.68 (0.13), residues: 1632 sheet: None (None), residues: 0 loop : -0.46 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 127 TYR 0.018 0.001 TYR J 545 PHE 0.016 0.001 PHE D 332 TRP 0.010 0.001 TRP D 379 HIS 0.005 0.001 HIS G 240 Details of bonding type rmsd covalent geometry : bond 0.00404 (17820) covalent geometry : angle 0.51487 (24072) hydrogen bonds : bond 0.04160 ( 1069) hydrogen bonds : angle 3.14848 ( 3183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7222 (m-90) cc_final: 0.6545 (m100) REVERT: A 286 ASP cc_start: 0.9016 (t0) cc_final: 0.8564 (t0) REVERT: B 38 ARG cc_start: 0.8686 (mtm110) cc_final: 0.8389 (mtm110) REVERT: C 65 MET cc_start: 0.8818 (mmt) cc_final: 0.8428 (mmt) REVERT: C 81 ARG cc_start: 0.7726 (mtp180) cc_final: 0.6661 (mmt180) REVERT: D 158 TRP cc_start: 0.7201 (m-90) cc_final: 0.6529 (m100) REVERT: D 286 ASP cc_start: 0.9027 (t0) cc_final: 0.8570 (t0) REVERT: E 18 SER cc_start: 0.8931 (t) cc_final: 0.8654 (p) REVERT: E 22 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7654 (mttp) REVERT: F 65 MET cc_start: 0.8812 (mmt) cc_final: 0.8425 (mmt) REVERT: F 81 ARG cc_start: 0.7662 (mtp180) cc_final: 0.6587 (mmt180) REVERT: G 158 TRP cc_start: 0.7186 (m-90) cc_final: 0.6522 (m100) REVERT: G 286 ASP cc_start: 0.9025 (t0) cc_final: 0.8568 (t0) REVERT: H 38 ARG cc_start: 0.8676 (mtm110) cc_final: 0.8375 (mtm110) REVERT: I 59 MET cc_start: 0.8676 (mtt) cc_final: 0.8466 (mtt) REVERT: I 81 ARG cc_start: 0.7693 (mtp180) cc_final: 0.6653 (mmt180) REVERT: J 158 TRP cc_start: 0.7136 (m-90) cc_final: 0.6482 (m100) REVERT: J 286 ASP cc_start: 0.9016 (t0) cc_final: 0.8545 (t0) REVERT: L 65 MET cc_start: 0.8821 (mmt) cc_final: 0.8430 (mmt) REVERT: L 81 ARG cc_start: 0.7707 (mtp180) cc_final: 0.6929 (ttp-170) outliers start: 37 outliers final: 31 residues processed: 295 average time/residue: 0.1627 time to fit residues: 67.0607 Evaluate side-chains 290 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 363 HIS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 41 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN E 144 GLN H 144 GLN L 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096904 restraints weight = 24157.010| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.37 r_work: 0.3099 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17820 Z= 0.134 Angle : 0.494 6.182 24072 Z= 0.262 Chirality : 0.039 0.124 2688 Planarity : 0.003 0.056 3028 Dihedral : 3.584 12.900 2396 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.86 % Allowed : 14.08 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.18), residues: 2140 helix: 1.78 (0.13), residues: 1632 sheet: None (None), residues: 0 loop : -0.42 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 127 TYR 0.014 0.001 TYR J 545 PHE 0.016 0.001 PHE G 332 TRP 0.011 0.001 TRP G 379 HIS 0.005 0.001 HIS D 240 Details of bonding type rmsd covalent geometry : bond 0.00320 (17820) covalent geometry : angle 0.49448 (24072) hydrogen bonds : bond 0.03836 ( 1069) hydrogen bonds : angle 3.06535 ( 3183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7078 (m-90) cc_final: 0.6502 (m100) REVERT: A 286 ASP cc_start: 0.9010 (t0) cc_final: 0.8565 (t0) REVERT: A 562 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7975 (ttp80) REVERT: B 38 ARG cc_start: 0.8696 (mtm110) cc_final: 0.8424 (mtm110) REVERT: B 54 ASN cc_start: 0.8686 (m110) cc_final: 0.8335 (m-40) REVERT: C 81 ARG cc_start: 0.7673 (mtp180) cc_final: 0.6635 (mmt180) REVERT: D 158 TRP cc_start: 0.7105 (m-90) cc_final: 0.6462 (m100) REVERT: D 286 ASP cc_start: 0.9018 (t0) cc_final: 0.8567 (t0) REVERT: D 562 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7977 (ttp80) REVERT: E 18 SER cc_start: 0.8919 (t) cc_final: 0.8698 (p) REVERT: E 22 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7755 (mttp) REVERT: F 81 ARG cc_start: 0.7628 (mtp180) cc_final: 0.6561 (mmt180) REVERT: G 158 TRP cc_start: 0.7087 (m-90) cc_final: 0.6448 (m100) REVERT: G 286 ASP cc_start: 0.9011 (t0) cc_final: 0.8562 (t0) REVERT: G 562 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7978 (ttp80) REVERT: H 18 SER cc_start: 0.8899 (t) cc_final: 0.8631 (p) REVERT: H 22 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7671 (mttp) REVERT: H 38 ARG cc_start: 0.8713 (mtm110) cc_final: 0.8437 (mtm110) REVERT: H 54 ASN cc_start: 0.8669 (m110) cc_final: 0.8311 (m-40) REVERT: I 81 ARG cc_start: 0.7603 (mtp180) cc_final: 0.6547 (mmt180) REVERT: J 158 TRP cc_start: 0.7078 (m-90) cc_final: 0.6463 (m100) REVERT: J 286 ASP cc_start: 0.9009 (t0) cc_final: 0.8558 (t0) REVERT: J 562 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7970 (ttp80) REVERT: K 22 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7706 (mttp) REVERT: L 81 ARG cc_start: 0.7609 (mtp180) cc_final: 0.6555 (mmt180) outliers start: 34 outliers final: 32 residues processed: 282 average time/residue: 0.1612 time to fit residues: 63.8350 Evaluate side-chains 288 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain G residue 363 HIS Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 214 CYS Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 376 GLN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 178 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 72 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 56 ASN I 98 ASN L 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099536 restraints weight = 24369.116| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.43 r_work: 0.3127 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17820 Z= 0.110 Angle : 0.471 6.402 24072 Z= 0.250 Chirality : 0.037 0.120 2688 Planarity : 0.003 0.057 3028 Dihedral : 3.453 13.189 2396 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.86 % Allowed : 14.25 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.18), residues: 2140 helix: 1.94 (0.13), residues: 1632 sheet: None (None), residues: 0 loop : -0.38 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 127 TYR 0.011 0.001 TYR J 545 PHE 0.015 0.001 PHE G 332 TRP 0.012 0.001 TRP D 379 HIS 0.005 0.001 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00253 (17820) covalent geometry : angle 0.47108 (24072) hydrogen bonds : bond 0.03547 ( 1069) hydrogen bonds : angle 2.95529 ( 3183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4492.10 seconds wall clock time: 77 minutes 21.62 seconds (4641.62 seconds total)