Starting phenix.real_space_refine on Fri Feb 14 17:10:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ka4_22758/02_2025/7ka4_22758.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ka4_22758/02_2025/7ka4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ka4_22758/02_2025/7ka4_22758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ka4_22758/02_2025/7ka4_22758.map" model { file = "/net/cci-nas-00/data/ceres_data/7ka4_22758/02_2025/7ka4_22758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ka4_22758/02_2025/7ka4_22758.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, D Time building chain proxies: 5.08, per 1000 atoms: 0.49 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.15 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: 3.57 Time building geometry restraints manager: 2.92 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.360 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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= 0.349 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (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 TRP 0.020 0.003 TRP A 147 HIS 0.003 0.001 HIS D 156 PHE 0.017 0.003 PHE A 144 TYR 0.015 0.002 TYR C 213 ARG 0.006 0.001 ARG A 55 *********************** 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 : 1.156 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: 1.5598 time to fit residues: 452.5130 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 : 1.116 ------------------------------------------------------------------------------- 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 114 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3872 r_free = 0.3872 target = 0.142874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116861 restraints weight = 14304.765| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.96 r_work: 0.3425 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10672 Z= 0.203 Angle : 0.608 9.556 14464 Z= 0.311 Chirality : 0.043 0.127 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.245 43.223 1476 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.33 % Allowed : 15.83 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1364 helix: 0.85 (0.18), residues: 688 sheet: -2.06 (0.35), residues: 200 loop : -0.49 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 147 HIS 0.001 0.000 HIS C 219 PHE 0.007 0.001 PHE C 144 TYR 0.014 0.001 TYR D 213 ARG 0.003 0.000 ARG D 330 *********************** 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 169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.129 Fit side-chains REVERT: C 41 LYS cc_start: 0.8025 (pptt) cc_final: 0.7761 (tmmt) REVERT: D 41 LYS cc_start: 0.8045 (pptt) cc_final: 0.7823 (pptt) outliers start: 37 outliers final: 16 residues processed: 158 average time/residue: 1.6446 time to fit residues: 275.1347 Evaluate side-chains 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 52 GLU 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 164 MET 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 126 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3828 r_free = 0.3828 target = 0.138906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112616 restraints weight = 14559.468| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.96 r_work: 0.3374 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10672 Z= 0.258 Angle : 0.585 7.627 14464 Z= 0.303 Chirality : 0.043 0.123 1644 Planarity : 0.004 0.035 1880 Dihedral : 4.624 20.429 1476 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.97 % Allowed : 14.84 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1364 helix: 1.47 (0.19), residues: 684 sheet: -2.02 (0.34), residues: 200 loop : -0.19 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 147 HIS 0.003 0.001 HIS D 2 PHE 0.007 0.001 PHE D 144 TYR 0.015 0.002 TYR D 213 ARG 0.007 0.001 ARG B 59 *********************** 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 154 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.157 Fit side-chains REVERT: A 41 LYS cc_start: 0.8051 (pptt) cc_final: 0.7747 (tmmt) REVERT: C 41 LYS cc_start: 0.8086 (pptt) cc_final: 0.7462 (ptmm) REVERT: D 41 LYS cc_start: 0.8019 (pptt) cc_final: 0.7734 (tmmt) REVERT: D 311 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8378 (tmmt) outliers start: 33 outliers final: 13 residues processed: 143 average time/residue: 1.5509 time to fit residues: 235.6415 Evaluate side-chains 129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 A residue 3 SER Chi-restraints excluded: chain A residue 52 GLU 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 164 MET 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 Chi-restraints excluded: chain D residue 311 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN C 44 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114443 restraints weight = 14409.216| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.96 r_work: 0.3400 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10672 Z= 0.182 Angle : 0.533 7.120 14464 Z= 0.275 Chirality : 0.041 0.119 1644 Planarity : 0.003 0.032 1880 Dihedral : 4.252 17.496 1472 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.61 % Allowed : 15.74 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1364 helix: 1.91 (0.19), residues: 680 sheet: -1.94 (0.34), residues: 200 loop : -0.04 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.001 0.000 HIS A 156 PHE 0.009 0.001 PHE D 144 TYR 0.013 0.001 TYR B 213 ARG 0.007 0.000 ARG B 59 *********************** 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 162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.195 Fit side-chains REVERT: A 41 LYS cc_start: 0.8063 (pptt) cc_final: 0.7424 (ptmm) REVERT: C 41 LYS cc_start: 0.8085 (pptt) cc_final: 0.7432 (ptmm) REVERT: D 41 LYS cc_start: 0.8016 (pptt) cc_final: 0.7713 (tmmt) REVERT: D 311 LYS cc_start: 0.8555 (tmtp) cc_final: 0.8324 (tmmt) REVERT: D 330 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7604 (mmp-170) outliers start: 29 outliers final: 16 residues processed: 151 average time/residue: 1.5221 time to fit residues: 245.2469 Evaluate side-chains 136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 63 LEU 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 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 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain D residue 3 SER 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 83 optimal weight: 0.0000 chunk 134 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN C 44 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113830 restraints weight = 14396.416| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.98 r_work: 0.3392 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10672 Z= 0.202 Angle : 0.533 7.237 14464 Z= 0.275 Chirality : 0.042 0.129 1644 Planarity : 0.003 0.031 1880 Dihedral : 4.128 15.076 1472 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.05 % Allowed : 15.56 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1364 helix: 2.16 (0.20), residues: 684 sheet: -1.91 (0.34), residues: 200 loop : -0.02 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 147 HIS 0.002 0.000 HIS D 2 PHE 0.008 0.001 PHE B 144 TYR 0.014 0.001 TYR D 213 ARG 0.005 0.000 ARG B 59 *********************** 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 184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 1.168 Fit side-chains REVERT: B 95 GLN cc_start: 0.8347 (tp-100) cc_final: 0.8127 (tp40) REVERT: B 329 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7638 (ptmt) REVERT: B 330 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7577 (mmp-170) REVERT: A 41 LYS cc_start: 0.8061 (pptt) cc_final: 0.7393 (ptmm) REVERT: C 41 LYS cc_start: 0.8067 (pptt) cc_final: 0.7451 (ptmm) REVERT: D 41 LYS cc_start: 0.8055 (pptt) cc_final: 0.7779 (tmmt) REVERT: D 189 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: D 311 LYS cc_start: 0.8511 (tmtp) cc_final: 0.8291 (tmmt) outliers start: 45 outliers final: 18 residues processed: 173 average time/residue: 1.5302 time to fit residues: 281.1986 Evaluate side-chains 145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 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 173 TYR Chi-restraints excluded: chain D residue 189 GLU 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 89 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3848 r_free = 0.3848 target = 0.140779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114864 restraints weight = 14401.963| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.97 r_work: 0.3409 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10672 Z= 0.174 Angle : 0.521 7.319 14464 Z= 0.268 Chirality : 0.041 0.124 1644 Planarity : 0.003 0.031 1880 Dihedral : 4.025 15.873 1472 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.42 % Allowed : 16.82 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1364 helix: 2.38 (0.20), residues: 684 sheet: -1.95 (0.34), residues: 200 loop : 0.06 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 147 HIS 0.001 0.000 HIS B 4 PHE 0.008 0.001 PHE D 144 TYR 0.013 0.001 TYR D 213 ARG 0.004 0.000 ARG B 59 *********************** 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 178 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: B 329 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7772 (ptmt) REVERT: B 330 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7576 (mmp-170) REVERT: A 41 LYS cc_start: 0.8043 (pptt) cc_final: 0.7375 (ptmm) REVERT: C 41 LYS cc_start: 0.8030 (pptt) cc_final: 0.7435 (ptmm) REVERT: C 42 ARG cc_start: 0.7386 (mtt180) cc_final: 0.7077 (mtt180) REVERT: D 41 LYS cc_start: 0.8049 (pptt) cc_final: 0.7786 (tmmt) REVERT: D 189 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: D 311 LYS cc_start: 0.8528 (tmtp) cc_final: 0.8293 (tmmt) outliers start: 38 outliers final: 20 residues processed: 166 average time/residue: 1.4022 time to fit residues: 248.7694 Evaluate side-chains 144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 63 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 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 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 60 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 68 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN C 44 GLN 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 = 0.3862 r_free = 0.3862 target = 0.141824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116250 restraints weight = 14554.136| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.97 r_work: 0.3420 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10672 Z= 0.164 Angle : 0.524 7.265 14464 Z= 0.270 Chirality : 0.040 0.126 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.907 13.865 1472 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.60 % Allowed : 17.09 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1364 helix: 2.55 (0.20), residues: 684 sheet: -1.90 (0.34), residues: 200 loop : 0.14 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 147 HIS 0.001 0.000 HIS C 245 PHE 0.009 0.001 PHE D 144 TYR 0.011 0.001 TYR B 213 ARG 0.004 0.000 ARG B 59 *********************** 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 171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 THR cc_start: 0.7957 (m) cc_final: 0.7663 (t) REVERT: B 329 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7842 (ptmt) REVERT: B 330 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7501 (mmp-170) REVERT: A 41 LYS cc_start: 0.8030 (pptt) cc_final: 0.7387 (ptmm) REVERT: A 42 ARG cc_start: 0.7301 (mtt180) cc_final: 0.7021 (mtt180) REVERT: C 41 LYS cc_start: 0.8023 (pptt) cc_final: 0.7409 (ptmm) REVERT: C 189 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: D 14 GLU cc_start: 0.7712 (pp20) cc_final: 0.7497 (pt0) REVERT: D 41 LYS cc_start: 0.8056 (pptt) cc_final: 0.7838 (tmmt) REVERT: D 311 LYS cc_start: 0.8532 (tmtp) cc_final: 0.8289 (tmmt) outliers start: 40 outliers final: 17 residues processed: 156 average time/residue: 1.4358 time to fit residues: 239.2075 Evaluate side-chains 145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 63 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 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 173 TYR Chi-restraints excluded: chain C residue 189 GLU 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 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 10 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3829 r_free = 0.3829 target = 0.139124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113458 restraints weight = 14483.517| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.94 r_work: 0.3384 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10672 Z= 0.239 Angle : 0.567 7.429 14464 Z= 0.291 Chirality : 0.042 0.132 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.074 14.730 1472 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.24 % Allowed : 17.45 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1364 helix: 2.39 (0.20), residues: 684 sheet: -1.92 (0.34), residues: 200 loop : 0.08 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 147 HIS 0.002 0.001 HIS B 245 PHE 0.008 0.001 PHE C 144 TYR 0.015 0.002 TYR D 213 ARG 0.003 0.000 ARG B 59 *********************** 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 168 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: B 329 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7780 (ptmt) REVERT: A 41 LYS cc_start: 0.8012 (pptt) cc_final: 0.7365 (ptmm) REVERT: A 189 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: A 329 LYS cc_start: 0.8388 (ptmt) cc_final: 0.8032 (ptmm) REVERT: C 41 LYS cc_start: 0.8026 (pptt) cc_final: 0.7444 (ptmm) REVERT: D 41 LYS cc_start: 0.8054 (pptt) cc_final: 0.7332 (ptmm) REVERT: D 189 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: D 241 GLN cc_start: 0.7707 (tt0) cc_final: 0.7501 (mt0) REVERT: D 311 LYS cc_start: 0.8524 (tmtp) cc_final: 0.8267 (tmmt) outliers start: 36 outliers final: 20 residues processed: 158 average time/residue: 1.3699 time to fit residues: 232.4117 Evaluate side-chains 150 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 189 GLU 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 173 TYR Chi-restraints excluded: chain A residue 189 GLU 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 30 LEU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 329 LYS 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 94 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 78 optimal weight: 0.0070 chunk 75 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN C 231 ASN D 231 ASN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115765 restraints weight = 14609.524| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.96 r_work: 0.3416 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10672 Z= 0.171 Angle : 0.534 7.489 14464 Z= 0.274 Chirality : 0.041 0.126 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.919 14.663 1472 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.88 % Allowed : 17.63 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1364 helix: 2.59 (0.20), residues: 684 sheet: -1.74 (0.34), residues: 200 loop : 0.11 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 147 HIS 0.001 0.000 HIS B 245 PHE 0.008 0.001 PHE D 144 TYR 0.012 0.001 TYR A 213 ARG 0.003 0.000 ARG B 59 *********************** 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 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 THR cc_start: 0.7967 (m) cc_final: 0.7688 (t) REVERT: B 329 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7869 (ptmt) REVERT: A 41 LYS cc_start: 0.8011 (pptt) cc_final: 0.7386 (ptmm) REVERT: A 42 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6893 (mtt180) REVERT: A 189 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: A 329 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8068 (ptmm) REVERT: C 41 LYS cc_start: 0.8044 (pptt) cc_final: 0.7439 (ptmm) REVERT: D 14 GLU cc_start: 0.7699 (pp20) cc_final: 0.7489 (pt0) REVERT: D 41 LYS cc_start: 0.8064 (pptt) cc_final: 0.7354 (ptmm) REVERT: D 189 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: D 311 LYS cc_start: 0.8499 (tmtp) cc_final: 0.8258 (tmmt) outliers start: 32 outliers final: 20 residues processed: 153 average time/residue: 1.4350 time to fit residues: 234.2184 Evaluate side-chains 142 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain B residue 63 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 52 GLU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU 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 30 LEU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 329 LYS 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 93 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN C 231 ASN D 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116959 restraints weight = 14527.085| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.97 r_work: 0.3432 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10672 Z= 0.166 Angle : 0.542 8.052 14464 Z= 0.279 Chirality : 0.040 0.123 1644 Planarity : 0.003 0.029 1880 Dihedral : 3.834 15.402 1472 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1364 helix: 2.63 (0.20), residues: 684 sheet: -1.69 (0.34), residues: 200 loop : 0.18 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 147 HIS 0.002 0.000 HIS D 245 PHE 0.008 0.001 PHE D 144 TYR 0.018 0.001 TYR A 327 ARG 0.003 0.000 ARG B 59 ********************** 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 155 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 329 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7766 (ptmt) REVERT: A 41 LYS cc_start: 0.8010 (pptt) cc_final: 0.7382 (ptmm) REVERT: A 42 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6894 (mtt180) REVERT: A 329 LYS cc_start: 0.8361 (ptmt) cc_final: 0.8070 (ptmm) REVERT: C 41 LYS cc_start: 0.8070 (pptt) cc_final: 0.7455 (ptmm) REVERT: D 14 GLU cc_start: 0.7757 (pp20) cc_final: 0.7543 (pt0) REVERT: D 41 LYS cc_start: 0.8049 (pptt) cc_final: 0.7335 (ptmm) REVERT: D 189 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7539 (tp30) REVERT: D 311 LYS cc_start: 0.8491 (tmtp) cc_final: 0.8245 (tmmt) outliers start: 29 outliers final: 18 residues processed: 147 average time/residue: 1.3521 time to fit residues: 212.9656 Evaluate side-chains 143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain B residue 63 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 30 LEU 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 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 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 5 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 45 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN B 231 ASN A 44 GLN A 231 ASN C 231 ASN D 231 ASN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116561 restraints weight = 14409.018| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.96 r_work: 0.3426 rms_B_bonded: 2.49 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: 0.8229 moved from start: 0.3341 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= 0.174 Angle : 0.535 7.577 14464 Z= 0.275 Chirality : 0.041 0.122 1644 Planarity : 0.003 0.029 1880 Dihedral : 3.828 17.438 1472 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.34 % Allowed : 18.53 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1364 helix: 2.59 (0.20), residues: 684 sheet: -1.73 (0.34), residues: 200 loop : 0.17 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 147 HIS 0.001 0.000 HIS B 4 PHE 0.008 0.001 PHE D 144 TYR 0.017 0.001 TYR C 327 ARG 0.003 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8034.24 seconds wall clock time: 142 minutes 44.37 seconds (8564.37 seconds total)