Starting phenix.real_space_refine on Fri Sep 11 16:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ka4_22758/09_2026/7ka4_22758.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ka4_22758/09_2026/7ka4_22758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ka4_22758/09_2026/7ka4_22758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ka4_22758/09_2026/7ka4_22758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ka4_22758/09_2026/7ka4_22758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ka4_22758/09_2026/7ka4_22758.map" } resolution = 2.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Restraints were copied for chains: A, C, D Time building chain proxies: 1.95, per 1000 atoms: 0.19 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 80.99, 104.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 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: 0.75 Conformation dependent library (CDL) restraints added in 301.6 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 55.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.521A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.658A pdb=" N ILE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.544A pdb=" N VAL B 69 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.595A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.509A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.556A pdb=" N THR B 226 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.778A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'A' and resid 8 through 23 removed outlier: 3.522A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.657A pdb=" N ILE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.544A pdb=" N VAL A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.596A pdb=" N LEU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.510A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.556A pdb=" N THR A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.777A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.522A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 47 removed outlier: 3.658A pdb=" N ILE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.544A pdb=" N VAL C 69 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.596A pdb=" N LEU C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 84' Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.509A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.556A pdb=" N THR C 226 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.778A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.522A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 3.657A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.545A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.596A pdb=" N LEU D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 84' Processing helix chain 'D' and resid 92 through 99 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.509A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 226 removed outlier: 3.555A pdb=" N THR D 226 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.777A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.793A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.792A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.793A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE C 185 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.793A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 512 hydrogen bonds defined for protein. 1512 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: 1.69 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3461 1.34 - 1.46: 1733 1.46 - 1.57: 5418 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.334 1.396 -0.063 2.34e-02 1.83e+03 7.15e+00 bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.334 1.396 -0.063 2.34e-02 1.83e+03 7.14e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.00e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 6.98e+00 bond pdb=" CB GLU D 318 " pdb=" CG GLU D 318 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 14181 2.60 - 5.20: 247 5.20 - 7.80: 28 7.80 - 10.40: 4 10.40 - 13.00: 4 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA GLU B 318 " pdb=" CB GLU B 318 " pdb=" CG GLU B 318 " ideal model delta sigma weight residual 114.10 127.10 -13.00 2.00e+00 2.50e-01 4.22e+01 angle pdb=" CA GLU A 318 " pdb=" CB GLU A 318 " pdb=" CG GLU A 318 " ideal model delta sigma weight residual 114.10 127.10 -13.00 2.00e+00 2.50e-01 4.22e+01 angle pdb=" CA GLU C 318 " pdb=" CB GLU C 318 " pdb=" CG GLU C 318 " ideal model delta sigma weight residual 114.10 127.07 -12.97 2.00e+00 2.50e-01 4.21e+01 angle pdb=" CA GLU D 318 " pdb=" CB GLU D 318 " pdb=" CG GLU D 318 " ideal model delta sigma weight residual 114.10 127.07 -12.97 2.00e+00 2.50e-01 4.20e+01 angle pdb=" CB GLU C 318 " pdb=" CG GLU C 318 " pdb=" CD GLU C 318 " ideal model delta sigma weight residual 112.60 119.36 -6.76 1.70e+00 3.46e-01 1.58e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 5900 17.17 - 34.34: 460 34.34 - 51.52: 100 51.52 - 68.69: 36 68.69 - 85.86: 8 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA LEU D 270 " pdb=" C LEU D 270 " pdb=" N SER D 271 " pdb=" CA SER D 271 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU B 270 " pdb=" C LEU B 270 " pdb=" N SER B 271 " pdb=" CA SER B 271 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 876 0.030 - 0.060: 433 0.060 - 0.090: 197 0.090 - 0.119: 106 0.119 - 0.149: 32 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA ASN A 70 " pdb=" N ASN A 70 " pdb=" C ASN A 70 " pdb=" CB ASN A 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ASN C 70 " pdb=" N ASN C 70 " pdb=" C ASN C 70 " pdb=" CB ASN C 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ASN D 70 " pdb=" N ASN D 70 " pdb=" C ASN D 70 " pdb=" CB ASN D 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 330 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ARG C 330 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 330 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA C 331 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 330 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C ARG B 330 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG B 330 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA B 331 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 330 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ARG A 330 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 330 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 331 " -0.017 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3743 2.88 - 3.38: 9972 3.38 - 3.89: 18607 3.89 - 4.39: 20834 4.39 - 4.90: 35200 Nonbonded interactions: 88356 Sorted by model distance: nonbonded pdb=" O GLN C 60 " pdb=" OG1 THR C 64 " model vdw 2.372 3.040 nonbonded pdb=" O GLN A 60 " pdb=" OG1 THR A 64 " model vdw 2.372 3.040 nonbonded pdb=" O GLN D 60 " pdb=" OG1 THR D 64 " model vdw 2.372 3.040 nonbonded pdb=" O GLN B 60 " pdb=" OG1 THR B 64 " model vdw 2.373 3.040 nonbonded pdb=" ND2 ASN A 119 " pdb=" OE2 GLU A 155 " model vdw 2.394 3.120 ... (remaining 88351 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 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.005 0.066 10672 Z= 0.245 Angle : 0.885 12.997 14464 Z= 0.498 Chirality : 0.048 0.149 1644 Planarity : 0.008 0.061 1880 Dihedral : 14.056 85.859 3984 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.96 % Allowed : 4.41 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.20 (0.19), residues: 1364 helix: -1.27 (0.15), residues: 680 sheet: -2.08 (0.34), residues: 204 loop : -1.10 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 55 TYR 0.015 0.002 TYR C 213 PHE 0.017 0.003 PHE A 144 TRP 0.020 0.003 TRP A 147 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 (10672) covalent geometry : angle 0.88537 / 0.50 (14464) hydrogen bonds : bond 0.14749 / 10.07 ( 512) hydrogen bonds : angle 6.39767 / 4.48 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.387 Fit side-chains REVERT: B 124 THR cc_start: 0.8805 (t) cc_final: 0.8555 (m) REVERT: A 124 THR cc_start: 0.8954 (t) cc_final: 0.8744 (m) outliers start: 44 outliers final: 4 residues processed: 274 average time/residue: 0.7060 time to fit residues: 205.1482 Evaluate side-chains 141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 175 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN B 125 GLN B 231 ASN A 44 GLN A 125 GLN A 231 ASN C 44 GLN C 125 GLN C 168 ASN C 231 ASN D 44 GLN D 125 GLN D 231 ASN D 241 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117808 restraints weight = 14330.024| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.95 r_work: 0.3441 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10672 Z= 0.129 Angle : 0.603 9.922 14464 Z= 0.308 Chirality : 0.042 0.121 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.201 42.904 1476 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.15 % Allowed : 15.74 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.12 (0.22), residues: 1364 helix: 0.90 (0.19), residues: 684 sheet: -2.08 (0.35), residues: 200 loop : -0.41 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 330 TYR 0.013 0.001 TYR D 213 PHE 0.008 0.001 PHE C 144 TRP 0.011 0.001 TRP C 147 HIS 0.001 0.000 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10672) covalent geometry : angle 0.60264 / 0.31 (14464) hydrogen bonds : bond 0.04599 / 3.04 ( 512) hydrogen bonds : angle 4.35317 / 3.07 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.472 Fit side-chains REVERT: A 41 LYS cc_start: 0.8023 (pptt) cc_final: 0.7762 (tmmt) REVERT: C 41 LYS cc_start: 0.8043 (pptt) cc_final: 0.7794 (tmmt) REVERT: D 41 LYS cc_start: 0.8044 (pptt) cc_final: 0.7824 (pptt) outliers start: 35 outliers final: 14 residues processed: 161 average time/residue: 0.6933 time to fit residues: 118.4471 Evaluate side-chains 126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 102 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 44 GLN A 231 ASN C 44 GLN C 168 ASN C 231 ASN D 231 ASN D 241 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117214 restraints weight = 14372.872| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.96 r_work: 0.3440 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10672 Z= 0.116 Angle : 0.540 7.012 14464 Z= 0.277 Chirality : 0.041 0.120 1644 Planarity : 0.004 0.032 1880 Dihedral : 4.397 20.024 1476 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.06 % Allowed : 14.84 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.67 (0.23), residues: 1364 helix: 1.70 (0.19), residues: 684 sheet: -2.05 (0.34), residues: 200 loop : -0.10 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 59 TYR 0.012 0.001 TYR B 213 PHE 0.007 0.001 PHE C 144 TRP 0.010 0.001 TRP D 147 HIS 0.002 0.000 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10672) covalent geometry : angle 0.54018 / 0.28 (14464) hydrogen bonds : bond 0.03999 / 2.65 ( 512) hydrogen bonds : angle 3.99174 / 2.81 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.412 Fit side-chains REVERT: A 41 LYS cc_start: 0.8055 (pptt) cc_final: 0.7420 (ptmm) REVERT: A 42 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7283 (mtt180) REVERT: C 41 LYS cc_start: 0.8070 (pptt) cc_final: 0.7426 (ptmm) REVERT: C 42 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7292 (mtt180) REVERT: D 36 THR cc_start: 0.7966 (m) cc_final: 0.7660 (t) REVERT: D 41 LYS cc_start: 0.7965 (pptt) cc_final: 0.7698 (tmmt) REVERT: D 303 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7549 (ttt90) outliers start: 34 outliers final: 12 residues processed: 159 average time/residue: 0.6496 time to fit residues: 110.1134 Evaluate side-chains 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 78 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.9333 > 50:) chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 44 GLN A 231 ASN C 44 GLN C 168 ASN C 231 ASN D 231 ASN D 241 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.142993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116680 restraints weight = 14475.072| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.99 r_work: 0.3434 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10672 Z= 0.108 Angle : 0.513 6.938 14464 Z= 0.263 Chirality : 0.041 0.118 1644 Planarity : 0.003 0.031 1880 Dihedral : 4.114 17.985 1472 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.16 % Allowed : 16.28 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.13 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 684 sheet: -1.92 (0.34), residues: 200 loop : 0.07 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 59 TYR 0.012 0.001 TYR B 213 PHE 0.007 0.001 PHE C 144 TRP 0.009 0.001 TRP C 147 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10672) covalent geometry : angle 0.51252 / 0.26 (14464) hydrogen bonds : bond 0.03715 / 2.45 ( 512) hydrogen bonds : angle 3.84102 / 2.70 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.416 Fit side-chains REVERT: B 329 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7689 (ptmt) REVERT: A 41 LYS cc_start: 0.7995 (pptt) cc_final: 0.7381 (ptmm) REVERT: C 41 LYS cc_start: 0.7991 (pptt) cc_final: 0.7318 (ptmm) REVERT: D 41 LYS cc_start: 0.7949 (pptt) cc_final: 0.7692 (tmmt) REVERT: D 303 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7522 (ttt90) outliers start: 24 outliers final: 12 residues processed: 155 average time/residue: 0.6409 time to fit residues: 106.1945 Evaluate side-chains 131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 44 GLN A 231 ASN C 44 GLN C 168 ASN C 231 ASN D 44 GLN D 231 ASN D 241 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114977 restraints weight = 14343.122| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.95 r_work: 0.3402 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.132 Angle : 0.527 6.939 14464 Z= 0.273 Chirality : 0.042 0.125 1644 Planarity : 0.003 0.032 1880 Dihedral : 4.066 14.101 1472 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.51 % Allowed : 16.46 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.30 (0.23), residues: 1364 helix: 2.27 (0.20), residues: 684 sheet: -1.83 (0.35), residues: 200 loop : 0.13 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 59 TYR 0.014 0.001 TYR B 213 PHE 0.007 0.001 PHE D 144 TRP 0.011 0.001 TRP A 147 HIS 0.002 0.000 HIS D 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10672) covalent geometry : angle 0.52704 / 0.27 (14464) hydrogen bonds : bond 0.04003 / 2.63 ( 512) hydrogen bonds : angle 3.83122 / 2.70 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.418 Fit side-chains REVERT: B 329 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7795 (ptmt) REVERT: B 330 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7579 (mmp-170) REVERT: A 41 LYS cc_start: 0.8054 (pptt) cc_final: 0.7383 (ptmm) REVERT: C 41 LYS cc_start: 0.8028 (pptt) cc_final: 0.7366 (ptmm) REVERT: C 330 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7546 (mmp-170) REVERT: D 41 LYS cc_start: 0.8002 (pptt) cc_final: 0.7742 (tmmt) outliers start: 39 outliers final: 18 residues processed: 157 average time/residue: 0.6502 time to fit residues: 108.7259 Evaluate side-chains 146 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.0040 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 44 GLN A 231 ASN C 44 GLN C 231 ASN D 44 GLN D 231 ASN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112347 restraints weight = 14556.870| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.95 r_work: 0.3368 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10672 Z= 0.174 Angle : 0.571 7.678 14464 Z= 0.293 Chirality : 0.043 0.129 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.212 14.955 1472 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.78 % Allowed : 15.92 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.18 (0.23), residues: 1364 helix: 2.18 (0.20), residues: 680 sheet: -1.94 (0.34), residues: 200 loop : 0.10 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.016 0.002 TYR C 213 PHE 0.007 0.001 PHE D 144 TRP 0.015 0.002 TRP A 147 HIS 0.003 0.001 HIS D 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (10672) covalent geometry : angle 0.57087 / 0.29 (14464) hydrogen bonds : bond 0.04454 / 2.94 ( 512) hydrogen bonds : angle 3.96495 / 2.79 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: B 329 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7806 (ptmt) REVERT: B 330 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7644 (mmp-170) REVERT: A 41 LYS cc_start: 0.8049 (pptt) cc_final: 0.7476 (ptmm) REVERT: C 41 LYS cc_start: 0.8055 (pptt) cc_final: 0.7472 (ptmm) REVERT: C 330 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7548 (mmp-170) REVERT: D 41 LYS cc_start: 0.8057 (pptt) cc_final: 0.7335 (ptmm) REVERT: D 189 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7525 (tp30) outliers start: 42 outliers final: 18 residues processed: 162 average time/residue: 0.5772 time to fit residues: 100.4797 Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 83 optimal weight: 0.0770 chunk 87 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 44 GLN A 231 ASN C 44 GLN C 231 ASN D 44 GLN D 231 ASN D 334 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116526 restraints weight = 14375.990| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.95 r_work: 0.3430 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10672 Z= 0.104 Angle : 0.515 7.234 14464 Z= 0.265 Chirality : 0.041 0.126 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.934 14.382 1472 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.69 % Allowed : 16.28 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.56 (0.24), residues: 1364 helix: 2.55 (0.20), residues: 684 sheet: -1.75 (0.34), residues: 200 loop : 0.15 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 59 TYR 0.011 0.001 TYR C 327 PHE 0.008 0.001 PHE D 144 TRP 0.008 0.001 TRP C 147 HIS 0.002 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (10672) covalent geometry : angle 0.51506 / 0.26 (14464) hydrogen bonds : bond 0.03537 / 2.34 ( 512) hydrogen bonds : angle 3.75636 / 2.65 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.462 Fit side-chains REVERT: B 36 THR cc_start: 0.7949 (m) cc_final: 0.7649 (t) REVERT: B 329 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7749 (ptmt) REVERT: B 330 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7517 (mmp-170) REVERT: A 41 LYS cc_start: 0.8021 (pptt) cc_final: 0.7416 (ptmm) REVERT: C 41 LYS cc_start: 0.8006 (pptt) cc_final: 0.7423 (ptmm) REVERT: C 330 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7414 (mmp-170) REVERT: D 41 LYS cc_start: 0.8001 (pptt) cc_final: 0.7745 (tmmt) outliers start: 41 outliers final: 20 residues processed: 163 average time/residue: 0.6286 time to fit residues: 109.5832 Evaluate side-chains 138 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 129 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 117 optimal weight: 0.0670 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 44 GLN A 231 ASN C 168 ASN C 231 ASN D 44 GLN D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116765 restraints weight = 14369.150| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.94 r_work: 0.3429 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10672 Z= 0.109 Angle : 0.528 7.217 14464 Z= 0.273 Chirality : 0.040 0.130 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.856 13.972 1472 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.33 % Allowed : 16.82 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.60 (0.24), residues: 1364 helix: 2.56 (0.20), residues: 684 sheet: -1.72 (0.34), residues: 200 loop : 0.21 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.013 0.001 TYR A 327 PHE 0.008 0.001 PHE A 144 TRP 0.008 0.001 TRP C 147 HIS 0.002 0.000 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10672) covalent geometry : angle 0.52837 / 0.27 (14464) hydrogen bonds : bond 0.03619 / 2.39 ( 512) hydrogen bonds : angle 3.71493 / 2.63 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.422 Fit side-chains REVERT: B 329 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7929 (ptmt) REVERT: A 41 LYS cc_start: 0.8028 (pptt) cc_final: 0.7428 (ptmm) REVERT: A 329 LYS cc_start: 0.8361 (ptmt) cc_final: 0.8035 (ptmm) REVERT: C 41 LYS cc_start: 0.8074 (pptt) cc_final: 0.7470 (ptmm) REVERT: D 41 LYS cc_start: 0.8016 (pptt) cc_final: 0.7761 (tmmt) outliers start: 37 outliers final: 22 residues processed: 148 average time/residue: 0.6288 time to fit residues: 99.9377 Evaluate side-chains 138 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 44 GLN A 231 ASN C 168 ASN C 231 ASN D 44 GLN D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116721 restraints weight = 14552.278| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.95 r_work: 0.3427 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10672 Z= 0.112 Angle : 0.535 7.548 14464 Z= 0.275 Chirality : 0.041 0.150 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.847 13.535 1472 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.79 % Allowed : 17.81 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.65 (0.24), residues: 1364 helix: 2.61 (0.20), residues: 684 sheet: -1.71 (0.34), residues: 200 loop : 0.22 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.014 0.001 TYR C 327 PHE 0.008 0.001 PHE D 144 TRP 0.008 0.001 TRP D 147 HIS 0.001 0.000 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10672) covalent geometry : angle 0.53516 / 0.27 (14464) hydrogen bonds : bond 0.03579 / 2.37 ( 512) hydrogen bonds : angle 3.69240 / 2.61 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8033 (pptt) cc_final: 0.7463 (ptmm) REVERT: A 329 LYS cc_start: 0.8339 (ptmt) cc_final: 0.8041 (ptmm) REVERT: C 41 LYS cc_start: 0.8055 (pptt) cc_final: 0.7449 (ptmm) REVERT: D 41 LYS cc_start: 0.7998 (pptt) cc_final: 0.7750 (tmmt) REVERT: D 189 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7529 (tp30) outliers start: 31 outliers final: 22 residues processed: 143 average time/residue: 0.6281 time to fit residues: 96.2188 Evaluate side-chains 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN A 231 ASN C 231 ASN D 44 GLN D 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115524 restraints weight = 14426.508| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.99 r_work: 0.3414 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10672 Z= 0.126 Angle : 0.556 7.757 14464 Z= 0.286 Chirality : 0.041 0.131 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.865 13.617 1472 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.61 % Allowed : 18.17 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.61 (0.24), residues: 1364 helix: 2.56 (0.20), residues: 684 sheet: -1.71 (0.34), residues: 200 loop : 0.21 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.016 0.001 TYR A 327 PHE 0.007 0.001 PHE D 144 TRP 0.010 0.001 TRP C 147 HIS 0.002 0.000 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10672) covalent geometry : angle 0.55618 / 0.29 (14464) hydrogen bonds : bond 0.03733 / 2.47 ( 512) hydrogen bonds : angle 3.72137 / 2.62 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 36 THR cc_start: 0.7916 (m) cc_final: 0.7635 (t) REVERT: B 41 LYS cc_start: 0.8264 (pptt) cc_final: 0.8022 (pptt) REVERT: A 41 LYS cc_start: 0.8097 (pptt) cc_final: 0.7509 (ptmm) REVERT: A 329 LYS cc_start: 0.8361 (ptmt) cc_final: 0.8044 (ptmm) REVERT: C 41 LYS cc_start: 0.8089 (pptt) cc_final: 0.7490 (ptmm) REVERT: D 41 LYS cc_start: 0.8053 (pptt) cc_final: 0.7356 (ptmm) REVERT: D 189 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7506 (tp30) outliers start: 29 outliers final: 20 residues processed: 134 average time/residue: 0.5855 time to fit residues: 84.3229 Evaluate side-chains 134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 GLN B 231 ASN A 231 ASN C 231 ASN D 44 GLN D 95 GLN D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116134 restraints weight = 14531.704| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.99 r_work: 0.3423 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10672 Z= 0.114 Angle : 0.536 7.566 14464 Z= 0.276 Chirality : 0.041 0.129 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.819 13.795 1472 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.43 % Allowed : 18.35 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.62 (0.24), residues: 1364 helix: 2.57 (0.20), residues: 684 sheet: -1.70 (0.34), residues: 200 loop : 0.22 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.015 0.001 TYR C 327 PHE 0.008 0.001 PHE D 144 TRP 0.009 0.001 TRP C 147 HIS 0.002 0.000 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (10672) covalent geometry : angle 0.53598 / 0.28 (14464) hydrogen bonds : bond 0.03625 / 2.40 ( 512) hydrogen bonds : angle 3.68712 / 2.60 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3692.73 seconds wall clock time: 63 minutes 49.81 seconds (3829.81 seconds total)