Starting phenix.real_space_refine on Mon Jul 28 14:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ka4_22758/07_2025/7ka4_22758.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ka4_22758/07_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_22758/07_2025/7ka4_22758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ka4_22758/07_2025/7ka4_22758.map" model { file = "/net/cci-nas-00/data/ceres_data/7ka4_22758/07_2025/7ka4_22758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ka4_22758/07_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-5711/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: 5.35, per 1000 atoms: 0.51 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: 2.55 Conformation dependent library (CDL) restraints added in 1.2 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: 1.24 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: 2.78 Time building geometry restraints manager: 2.93 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: 0.07 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 24.440 Find NCS groups from input model: 0.190 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:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- 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= 0.245 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.14749 ( 512) hydrogen bonds : angle 6.39767 ( 1512) covalent geometry : bond 0.00538 (10672) covalent geometry : angle 0.88537 (14464) *********************** 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 : 1.170 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: 1.4565 time to fit residues: 422.8954 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 : 1.170 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116861 restraints weight = 14304.762| |-----------------------------------------------------------------------------| 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= 0.137 Angle : 0.608 9.556 14464 Z= 0.311 Chirality : 0.043 0.127 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.245 43.222 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 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 512) hydrogen bonds : angle 4.38097 ( 1512) covalent geometry : bond 0.00310 (10672) covalent geometry : angle 0.60805 (14464) *********************** 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 : 1.147 Fit side-chains REVERT: C 41 LYS cc_start: 0.8052 (pptt) cc_final: 0.7791 (tmmt) REVERT: D 41 LYS cc_start: 0.8063 (pptt) cc_final: 0.7848 (pptt) outliers start: 37 outliers final: 16 residues processed: 158 average time/residue: 1.5724 time to fit residues: 263.5274 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 : 1.319 ------------------------------------------------------------------------------- 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: 0.6980 chunk 105 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 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: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.140091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113785 restraints weight = 14520.799| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.96 r_work: 0.3392 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10672 Z= 0.155 Angle : 0.571 7.485 14464 Z= 0.295 Chirality : 0.042 0.121 1644 Planarity : 0.004 0.034 1880 Dihedral : 4.624 22.950 1476 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.88 % Allowed : 15.29 % Favored : 81.83 % 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: 0.51 (0.23), residues: 1364 helix: 1.52 (0.19), residues: 684 sheet: -2.04 (0.34), residues: 200 loop : -0.17 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 147 HIS 0.003 0.001 HIS D 2 PHE 0.007 0.001 PHE D 144 TYR 0.014 0.002 TYR A 213 ARG 0.007 0.000 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 512) hydrogen bonds : angle 4.12554 ( 1512) covalent geometry : bond 0.00361 (10672) covalent geometry : angle 0.57131 (14464) *********************** 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 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.294 Fit side-chains REVERT: A 41 LYS cc_start: 0.8038 (pptt) cc_final: 0.7751 (tmmt) REVERT: C 41 LYS cc_start: 0.8058 (pptt) cc_final: 0.7431 (ptmm) REVERT: C 42 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7229 (mtt180) REVERT: D 41 LYS cc_start: 0.7990 (pptt) cc_final: 0.7725 (tmmt) REVERT: D 311 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8374 (tmmt) outliers start: 32 outliers final: 12 residues processed: 148 average time/residue: 1.4513 time to fit residues: 228.8774 Evaluate side-chains 131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 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 = 0.3873 r_free = 0.3873 target = 0.142486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116399 restraints weight = 14343.057| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.96 r_work: 0.3428 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2644 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= 0.105 Angle : 0.510 8.288 14464 Z= 0.263 Chirality : 0.040 0.119 1644 Planarity : 0.003 0.031 1880 Dihedral : 4.137 17.691 1472 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.43 % Allowed : 16.28 % Favored : 81.29 % 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: 1.04 (0.23), residues: 1364 helix: 2.05 (0.19), residues: 684 sheet: -1.97 (0.34), residues: 200 loop : 0.03 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 147 HIS 0.001 0.000 HIS D 196 PHE 0.008 0.001 PHE D 144 TYR 0.010 0.001 TYR C 213 ARG 0.006 0.000 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 512) hydrogen bonds : angle 3.84842 ( 1512) covalent geometry : bond 0.00238 (10672) covalent geometry : angle 0.50998 (14464) *********************** 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 167 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.227 Fit side-chains REVERT: A 41 LYS cc_start: 0.8022 (pptt) cc_final: 0.7382 (ptmm) REVERT: C 41 LYS cc_start: 0.8050 (pptt) cc_final: 0.7407 (ptmm) REVERT: D 41 LYS cc_start: 0.8009 (pptt) cc_final: 0.7737 (tmmt) REVERT: D 311 LYS cc_start: 0.8555 (tmtp) cc_final: 0.8334 (tmmt) REVERT: D 330 ARG cc_start: 0.7804 (mmm160) cc_final: 0.7571 (mmp-170) outliers start: 27 outliers final: 12 residues processed: 158 average time/residue: 1.4635 time to fit residues: 246.7073 Evaluate side-chains 132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 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 83 optimal weight: 0.0270 chunk 134 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.1042 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.140548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114978 restraints weight = 14349.221| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.95 r_work: 0.3403 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2810 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= 0.128 Angle : 0.527 7.140 14464 Z= 0.272 Chirality : 0.041 0.128 1644 Planarity : 0.003 0.031 1880 Dihedral : 4.056 14.058 1472 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.33 % Allowed : 17.45 % 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: 1.25 (0.23), residues: 1364 helix: 2.25 (0.20), residues: 684 sheet: -1.87 (0.34), residues: 200 loop : 0.07 (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 D 144 TYR 0.013 0.001 TYR B 213 ARG 0.004 0.000 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 512) hydrogen bonds : angle 3.84670 ( 1512) covalent geometry : bond 0.00299 (10672) covalent geometry : angle 0.52727 (14464) *********************** 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 170 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.245 Fit side-chains REVERT: A 41 LYS cc_start: 0.8009 (pptt) cc_final: 0.7745 (tmmt) REVERT: C 41 LYS cc_start: 0.8041 (pptt) cc_final: 0.7381 (ptmm) REVERT: D 41 LYS cc_start: 0.8026 (pptt) cc_final: 0.7753 (tmmt) REVERT: D 189 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: D 311 LYS cc_start: 0.8506 (tmtp) cc_final: 0.8273 (tmmt) outliers start: 37 outliers final: 16 residues processed: 157 average time/residue: 1.5366 time to fit residues: 256.4633 Evaluate side-chains 138 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 125 optimal weight: 0.0030 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 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 = 0.3868 r_free = 0.3868 target = 0.142490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116462 restraints weight = 14465.870| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.99 r_work: 0.3426 rms_B_bonded: 2.51 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: 0.8232 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10672 Z= 0.104 Angle : 0.503 7.248 14464 Z= 0.259 Chirality : 0.040 0.125 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.918 14.501 1472 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.87 % Allowed : 16.55 % Favored : 79.59 % 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: 1.51 (0.24), residues: 1364 helix: 2.52 (0.20), residues: 684 sheet: -1.84 (0.35), 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 D 219 PHE 0.008 0.001 PHE D 144 TYR 0.011 0.001 TYR D 213 ARG 0.004 0.000 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 512) hydrogen bonds : angle 3.72211 ( 1512) covalent geometry : bond 0.00237 (10672) covalent geometry : angle 0.50307 (14464) *********************** 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 174 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 1.249 Fit side-chains REVERT: B 36 THR cc_start: 0.7861 (m) cc_final: 0.7595 (t) REVERT: B 330 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7586 (mmp-170) REVERT: A 41 LYS cc_start: 0.7980 (pptt) cc_final: 0.7715 (tmmt) REVERT: A 189 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: C 41 LYS cc_start: 0.8028 (pptt) cc_final: 0.7436 (ptmm) REVERT: C 42 ARG cc_start: 0.7360 (mtt180) cc_final: 0.7047 (mtt180) REVERT: C 189 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: D 41 LYS cc_start: 0.8037 (pptt) cc_final: 0.7776 (tmmt) REVERT: D 189 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: D 311 LYS cc_start: 0.8502 (tmtp) cc_final: 0.8264 (tmmt) outliers start: 43 outliers final: 21 residues processed: 159 average time/residue: 1.3612 time to fit residues: 231.4840 Evaluate side-chains 147 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 189 GLU 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 189 GLU 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 60 optimal weight: 0.2980 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 130 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.142289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116054 restraints weight = 14575.051| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.00 r_work: 0.3422 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3099 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= 0.114 Angle : 0.529 7.143 14464 Z= 0.274 Chirality : 0.041 0.127 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.874 13.877 1472 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.14 % Allowed : 16.01 % 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 (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: 1.55 (0.24), residues: 1364 helix: 2.55 (0.20), residues: 684 sheet: -1.83 (0.35), residues: 200 loop : 0.17 (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 C 245 PHE 0.008 0.001 PHE D 144 TYR 0.013 0.001 TYR B 213 ARG 0.004 0.000 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 512) hydrogen bonds : angle 3.70414 ( 1512) covalent geometry : bond 0.00264 (10672) covalent geometry : angle 0.52947 (14464) *********************** 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 172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 1.234 Fit side-chains REVERT: B 320 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.6012 (tt) REVERT: B 330 ARG cc_start: 0.7809 (mmm160) cc_final: 0.7585 (mmp-170) REVERT: A 41 LYS cc_start: 0.8010 (pptt) cc_final: 0.7754 (tmmt) REVERT: A 329 LYS cc_start: 0.8347 (ptmt) cc_final: 0.7981 (ptmm) REVERT: C 41 LYS cc_start: 0.8014 (pptt) cc_final: 0.7407 (ptmm) REVERT: C 189 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: D 41 LYS cc_start: 0.8027 (pptt) cc_final: 0.7767 (tmmt) REVERT: D 311 LYS cc_start: 0.8495 (tmtp) cc_final: 0.8263 (tmmt) outliers start: 46 outliers final: 22 residues processed: 155 average time/residue: 1.7704 time to fit residues: 293.3858 Evaluate side-chains 140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain B residue 329 LYS 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 164 MET 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 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 10 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.142678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116959 restraints weight = 14382.998| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.97 r_work: 0.3431 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10672 Z= 0.109 Angle : 0.527 7.363 14464 Z= 0.271 Chirality : 0.040 0.124 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.837 14.074 1472 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.42 % Allowed : 17.09 % 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: 1.62 (0.24), residues: 1364 helix: 2.61 (0.20), residues: 684 sheet: -1.80 (0.35), residues: 200 loop : 0.21 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 147 HIS 0.002 0.000 HIS A 245 PHE 0.008 0.001 PHE D 144 TYR 0.016 0.001 TYR A 327 ARG 0.015 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 512) hydrogen bonds : angle 3.64689 ( 1512) covalent geometry : bond 0.00254 (10672) covalent geometry : angle 0.52686 (14464) *********************** 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: 38 poor density : 122 time to evaluate : 2.392 Fit side-chains revert: symmetry clash REVERT: B 320 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5958 (tt) REVERT: B 330 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7544 (mmp-170) REVERT: A 329 LYS cc_start: 0.8363 (ptmt) cc_final: 0.7997 (ptmm) REVERT: C 41 LYS cc_start: 0.8000 (pptt) cc_final: 0.7414 (ptmm) REVERT: D 41 LYS cc_start: 0.7998 (pptt) cc_final: 0.7745 (tmmt) REVERT: D 189 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: D 206 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8241 (mm-30) REVERT: D 311 LYS cc_start: 0.8498 (tmtp) cc_final: 0.8249 (tmmt) outliers start: 38 outliers final: 21 residues processed: 144 average time/residue: 1.7957 time to fit residues: 276.1872 Evaluate side-chains 143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 44 GLN 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 = 0.3858 r_free = 0.3858 target = 0.141618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115707 restraints weight = 14597.253| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.99 r_work: 0.3413 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10672 Z= 0.125 Angle : 0.550 7.559 14464 Z= 0.282 Chirality : 0.041 0.128 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.881 13.811 1472 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.06 % Allowed : 17.72 % 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: 1.57 (0.24), residues: 1364 helix: 2.57 (0.20), residues: 684 sheet: -1.83 (0.35), residues: 200 loop : 0.19 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.001 0.000 HIS D 2 PHE 0.007 0.001 PHE D 144 TYR 0.016 0.001 TYR C 327 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 512) hydrogen bonds : angle 3.70394 ( 1512) covalent geometry : bond 0.00295 (10672) covalent geometry : angle 0.55002 (14464) *********************** 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 156 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: B 320 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.6029 (tt) REVERT: B 330 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7581 (mmp-170) REVERT: A 329 LYS cc_start: 0.8374 (ptmt) cc_final: 0.8075 (ptmm) REVERT: C 14 GLU cc_start: 0.7701 (pp20) cc_final: 0.7448 (pt0) REVERT: C 41 LYS cc_start: 0.8058 (pptt) cc_final: 0.7459 (ptmm) REVERT: C 329 LYS cc_start: 0.8370 (ptmt) cc_final: 0.7997 (ptmm) REVERT: D 41 LYS cc_start: 0.8028 (pptt) cc_final: 0.7775 (tmmt) REVERT: D 189 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: D 311 LYS cc_start: 0.8498 (tmtp) cc_final: 0.8252 (tmmt) outliers start: 34 outliers final: 20 residues processed: 146 average time/residue: 1.3519 time to fit residues: 211.8516 Evaluate side-chains 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER 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 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 93 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 44 GLN 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 = 0.3869 r_free = 0.3869 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116140 restraints weight = 14519.321| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.01 r_work: 0.3423 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10672 Z= 0.116 Angle : 0.540 7.643 14464 Z= 0.278 Chirality : 0.041 0.124 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.851 14.413 1472 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.88 % Allowed : 17.90 % 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: 1.62 (0.24), residues: 1364 helix: 2.59 (0.20), residues: 684 sheet: -1.66 (0.34), residues: 200 loop : 0.15 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 147 HIS 0.002 0.000 HIS D 245 PHE 0.008 0.001 PHE D 144 TYR 0.013 0.001 TYR B 213 ARG 0.003 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 512) hydrogen bonds : angle 3.69371 ( 1512) covalent geometry : bond 0.00272 (10672) covalent geometry : angle 0.53981 (14464) ********************** 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 153 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: B 36 THR cc_start: 0.7831 (m) cc_final: 0.7563 (t) REVERT: B 320 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.6019 (tt) REVERT: A 206 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8293 (mm-30) REVERT: A 329 LYS cc_start: 0.8375 (ptmt) cc_final: 0.8070 (ptmm) REVERT: C 14 GLU cc_start: 0.7708 (pp20) cc_final: 0.7452 (pt0) REVERT: C 41 LYS cc_start: 0.8057 (pptt) cc_final: 0.7460 (ptmm) REVERT: C 329 LYS cc_start: 0.8365 (ptmt) cc_final: 0.8064 (ptmm) REVERT: D 41 LYS cc_start: 0.8001 (pptt) cc_final: 0.7300 (ptmm) REVERT: D 189 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: D 311 LYS cc_start: 0.8475 (tmtp) cc_final: 0.8229 (tmmt) outliers start: 32 outliers final: 20 residues processed: 142 average time/residue: 1.4502 time to fit residues: 220.8811 Evaluate side-chains 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 320 LEU 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 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 5 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 43 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 231 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117733 restraints weight = 14377.303| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.96 r_work: 0.3442 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10672 Z= 0.106 Angle : 0.534 7.612 14464 Z= 0.276 Chirality : 0.040 0.122 1644 Planarity : 0.003 0.030 1880 Dihedral : 3.783 13.677 1472 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.34 % Allowed : 18.71 % Favored : 78.96 % 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: 1.68 (0.24), residues: 1364 helix: 2.64 (0.20), residues: 684 sheet: -1.63 (0.34), residues: 200 loop : 0.20 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 147 HIS 0.002 0.000 HIS C 245 PHE 0.008 0.001 PHE D 144 TYR 0.016 0.001 TYR C 327 ARG 0.003 0.000 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 512) hydrogen bonds : angle 3.64823 ( 1512) covalent geometry : bond 0.00245 (10672) covalent geometry : angle 0.53441 (14464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8522.24 seconds wall clock time: 148 minutes 42.03 seconds (8922.03 seconds total)