Starting phenix.real_space_refine on Thu Sep 18 07:12:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pwp_20510/09_2025/6pwp_20510.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pwp_20510/09_2025/6pwp_20510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pwp_20510/09_2025/6pwp_20510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pwp_20510/09_2025/6pwp_20510.map" model { file = "/net/cci-nas-00/data/ceres_data/6pwp_20510/09_2025/6pwp_20510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pwp_20510/09_2025/6pwp_20510.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 49 5.16 5 C 9548 2.51 5 N 2590 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14903 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2129 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 5, 'TRANS': 274} Time building chain proxies: 3.53, per 1000 atoms: 0.24 Number of scatterers: 14903 At special positions: 0 Unit cell: (98.952, 97.888, 151.088, 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 49 16.00 O 2716 8.00 N 2590 7.00 C 9548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 716.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 57.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 20 through 58 removed outlier: 3.855A pdb=" N TYR A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL B 6 " --> pdb=" O GLU B 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 7' Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.863A pdb=" N VAL C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 7' Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 7' Processing helix chain 'D' and resid 10 through 14 Processing helix chain 'D' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.691A pdb=" N ALA D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 243 through 265 removed outlier: 4.617A pdb=" N GLN D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.864A pdb=" N VAL E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 7' Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 20 through 58 removed outlier: 3.855A pdb=" N TYR E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.863A pdb=" N VAL F 6 " --> pdb=" O GLU F 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 7' Processing helix chain 'F' and resid 10 through 14 Processing helix chain 'F' and resid 20 through 58 removed outlier: 3.855A pdb=" N TYR F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.690A pdb=" N ALA F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU F 254 " --> pdb=" O TYR F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.863A pdb=" N VAL G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 7' Processing helix chain 'G' and resid 10 through 14 Processing helix chain 'G' and resid 20 through 58 removed outlier: 3.854A pdb=" N TYR G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 128 removed outlier: 4.561A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.689A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 243 through 265 removed outlier: 4.618A pdb=" N GLN G 247 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU G 254 " --> pdb=" O TYR G 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 3.580A pdb=" N VAL A 136 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 145 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 136 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL B 145 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG B 156 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 136 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL C 145 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG C 156 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 136 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL D 145 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG D 156 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 136 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL E 145 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG E 156 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 162 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 136 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL F 145 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ARG F 156 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 136 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL G 145 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG G 156 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE G 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 276 removed outlier: 3.914A pdb=" N ASN B 276 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 275 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN C 276 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 275 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN D 276 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN E 276 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 275 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN F 276 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 275 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN G 276 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N MET G 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP A 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL G 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN A 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 7.389A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 7.389A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 7.388A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2901 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: 2.63 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4991 1.35 - 1.47: 3246 1.47 - 1.59: 6757 1.59 - 1.71: 0 1.71 - 1.83: 98 Bond restraints: 15092 Sorted by residual: bond pdb=" N GLY E 229 " pdb=" CA GLY E 229 " ideal model delta sigma weight residual 1.445 1.476 -0.031 9.20e-03 1.18e+04 1.15e+01 bond pdb=" N GLU E 227 " pdb=" CA GLU E 227 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.16e-02 7.43e+03 8.03e+00 bond pdb=" N GLU B 227 " pdb=" CA GLU B 227 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.16e-02 7.43e+03 7.45e+00 bond pdb=" N GLU C 227 " pdb=" CA GLU C 227 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.16e-02 7.43e+03 7.28e+00 bond pdb=" N GLU D 227 " pdb=" CA GLU D 227 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.16e-02 7.43e+03 7.18e+00 ... (remaining 15087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18317 1.26 - 2.52: 1834 2.52 - 3.77: 249 3.77 - 5.03: 57 5.03 - 6.29: 25 Bond angle restraints: 20482 Sorted by residual: angle pdb=" CA GLY D 229 " pdb=" C GLY D 229 " pdb=" O GLY D 229 " ideal model delta sigma weight residual 121.90 118.06 3.84 1.02e+00 9.61e-01 1.42e+01 angle pdb=" CA GLY E 229 " pdb=" C GLY E 229 " pdb=" O GLY E 229 " ideal model delta sigma weight residual 122.33 118.19 4.14 1.11e+00 8.12e-01 1.39e+01 angle pdb=" CA GLY B 229 " pdb=" C GLY B 229 " pdb=" O GLY B 229 " ideal model delta sigma weight residual 121.90 118.12 3.78 1.02e+00 9.61e-01 1.37e+01 angle pdb=" CA GLY A 229 " pdb=" C GLY A 229 " pdb=" O GLY A 229 " ideal model delta sigma weight residual 121.90 118.14 3.76 1.02e+00 9.61e-01 1.36e+01 angle pdb=" CA GLY C 229 " pdb=" C GLY C 229 " pdb=" O GLY C 229 " ideal model delta sigma weight residual 121.90 118.16 3.74 1.02e+00 9.61e-01 1.34e+01 ... (remaining 20477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 8133 16.14 - 32.28: 728 32.28 - 48.42: 133 48.42 - 64.56: 36 64.56 - 80.70: 21 Dihedral angle restraints: 9051 sinusoidal: 3444 harmonic: 5607 Sorted by residual: dihedral pdb=" CA GLN D 149 " pdb=" C GLN D 149 " pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta harmonic sigma weight residual -180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN C 149 " pdb=" C GLN C 149 " pdb=" N ILE C 150 " pdb=" CA ILE C 150 " ideal model delta harmonic sigma weight residual 180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN G 149 " pdb=" C GLN G 149 " pdb=" N ILE G 150 " pdb=" CA ILE G 150 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 9048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2241 0.077 - 0.154: 253 0.154 - 0.232: 12 0.232 - 0.309: 0 0.309 - 0.386: 7 Chirality restraints: 2513 Sorted by residual: chirality pdb=" CG LEU B 225 " pdb=" CB LEU B 225 " pdb=" CD1 LEU B 225 " pdb=" CD2 LEU B 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CG LEU A 225 " pdb=" CB LEU A 225 " pdb=" CD1 LEU A 225 " pdb=" CD2 LEU A 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CG LEU F 225 " pdb=" CB LEU F 225 " pdb=" CD1 LEU F 225 " pdb=" CD2 LEU F 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 2510 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 226 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ASN E 226 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN E 226 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU E 227 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 226 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C ASN B 226 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN B 226 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU B 227 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 226 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C ASN D 226 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN D 226 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 227 " 0.017 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 403 2.66 - 3.22: 18114 3.22 - 3.78: 24893 3.78 - 4.34: 32109 4.34 - 4.90: 48902 Nonbonded interactions: 124421 Sorted by model distance: nonbonded pdb=" OD1 ASP B 262 " pdb=" N ALA B 263 " model vdw 2.096 3.120 nonbonded pdb=" OD1 ASP C 262 " pdb=" N ALA C 263 " model vdw 2.096 3.120 nonbonded pdb=" OD1 ASP D 262 " pdb=" N ALA D 263 " model vdw 2.096 3.120 nonbonded pdb=" OD1 ASP F 262 " pdb=" N ALA F 263 " model vdw 2.097 3.120 nonbonded pdb=" OD1 ASP G 262 " pdb=" N ALA G 263 " model vdw 2.097 3.120 ... (remaining 124416 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.140 Find NCS groups from input model: 0.140 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.010 0.061 15092 Z= 0.505 Angle : 0.856 6.289 20482 Z= 0.535 Chirality : 0.051 0.386 2513 Planarity : 0.004 0.035 2604 Dihedral : 13.542 80.704 5439 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.31 % Allowed : 2.64 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.14), residues: 1946 helix: -1.62 (0.13), residues: 973 sheet: -2.80 (0.24), residues: 273 loop : -3.43 (0.16), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 131 TYR 0.011 0.002 TYR D 250 PHE 0.013 0.002 PHE E 127 TRP 0.004 0.001 TRP B 240 Details of bonding type rmsd covalent geometry : bond 0.00952 (15092) covalent geometry : angle 0.85643 (20482) hydrogen bonds : bond 0.18007 ( 995) hydrogen bonds : angle 6.90683 ( 2901) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8986 (ppp) cc_final: 0.8663 (ppp) REVERT: A 169 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9304 (ttmt) REVERT: B 155 MET cc_start: 0.9020 (ppp) cc_final: 0.8617 (ppp) REVERT: B 169 LYS cc_start: 0.9497 (ttmm) cc_final: 0.9239 (ttpt) REVERT: C 155 MET cc_start: 0.8983 (ppp) cc_final: 0.8674 (ppp) REVERT: D 155 MET cc_start: 0.8885 (ppp) cc_final: 0.8541 (ppp) REVERT: D 169 LYS cc_start: 0.9568 (ttmm) cc_final: 0.9315 (ttmt) REVERT: E 155 MET cc_start: 0.9038 (ppp) cc_final: 0.8685 (ppp) REVERT: E 169 LYS cc_start: 0.9583 (ttmm) cc_final: 0.9319 (ttmt) REVERT: F 155 MET cc_start: 0.9023 (ppp) cc_final: 0.8659 (ppp) REVERT: G 155 MET cc_start: 0.9036 (ppp) cc_final: 0.8692 (ppp) outliers start: 5 outliers final: 0 residues processed: 96 average time/residue: 0.1200 time to fit residues: 17.8743 Evaluate side-chains 68 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 226 ASN C 226 ASN D 226 ASN E 226 ASN F 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.024606 restraints weight = 141671.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025362 restraints weight = 85309.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.025916 restraints weight = 61065.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.026339 restraints weight = 49137.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.026524 restraints weight = 41640.888| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15092 Z= 0.156 Angle : 0.612 8.872 20482 Z= 0.331 Chirality : 0.043 0.140 2513 Planarity : 0.003 0.027 2604 Dihedral : 4.849 22.536 2121 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.17), residues: 1946 helix: 0.77 (0.15), residues: 1029 sheet: -0.91 (0.30), residues: 210 loop : -2.90 (0.19), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 259 TYR 0.012 0.001 TYR G 194 PHE 0.014 0.002 PHE F 261 TRP 0.014 0.002 TRP B 16 Details of bonding type rmsd covalent geometry : bond 0.00307 (15092) covalent geometry : angle 0.61213 (20482) hydrogen bonds : bond 0.05341 ( 995) hydrogen bonds : angle 4.60540 ( 2901) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9605 (ptt) cc_final: 0.9332 (mmm) REVERT: A 221 MET cc_start: 0.8710 (pmm) cc_final: 0.8124 (mpp) REVERT: B 47 MET cc_start: 0.9626 (ptp) cc_final: 0.9309 (mmm) REVERT: B 221 MET cc_start: 0.8706 (pmm) cc_final: 0.8300 (mpp) REVERT: C 47 MET cc_start: 0.9650 (ptt) cc_final: 0.9416 (mmm) REVERT: C 221 MET cc_start: 0.8567 (pmm) cc_final: 0.8264 (mpp) REVERT: D 47 MET cc_start: 0.9667 (ptt) cc_final: 0.9341 (mmm) REVERT: D 221 MET cc_start: 0.8676 (pmm) cc_final: 0.8422 (mpp) REVERT: E 47 MET cc_start: 0.9651 (ptt) cc_final: 0.9375 (mmm) REVERT: F 221 MET cc_start: 0.8636 (pmm) cc_final: 0.8278 (mpp) REVERT: G 47 MET cc_start: 0.9609 (mtm) cc_final: 0.9397 (mmm) REVERT: G 221 MET cc_start: 0.8676 (pmm) cc_final: 0.8296 (mpp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1102 time to fit residues: 17.9190 Evaluate side-chains 75 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 179 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 96 optimal weight: 0.0050 chunk 148 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 234 ASN A 247 GLN B 226 ASN B 234 ASN C 226 ASN C 234 ASN D 226 ASN D 234 ASN E 226 ASN E 234 ASN F 226 ASN F 234 ASN G 234 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.033038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.023773 restraints weight = 142369.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.024514 restraints weight = 87690.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.025017 restraints weight = 63604.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.025402 restraints weight = 51896.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025709 restraints weight = 43766.882| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15092 Z= 0.225 Angle : 0.613 8.480 20482 Z= 0.331 Chirality : 0.042 0.145 2513 Planarity : 0.004 0.029 2604 Dihedral : 4.746 16.832 2121 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.19), residues: 1946 helix: 1.27 (0.16), residues: 1022 sheet: -0.67 (0.31), residues: 224 loop : -2.38 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 131 TYR 0.013 0.002 TYR G 194 PHE 0.013 0.002 PHE G 268 TRP 0.026 0.002 TRP C 16 Details of bonding type rmsd covalent geometry : bond 0.00448 (15092) covalent geometry : angle 0.61312 (20482) hydrogen bonds : bond 0.04147 ( 995) hydrogen bonds : angle 4.60665 ( 2901) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9573 (ptt) cc_final: 0.9352 (mmm) REVERT: B 47 MET cc_start: 0.9619 (ptp) cc_final: 0.9378 (mmm) REVERT: D 47 MET cc_start: 0.9640 (ptt) cc_final: 0.9410 (mmm) REVERT: E 47 MET cc_start: 0.9627 (ptt) cc_final: 0.9417 (mmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1029 time to fit residues: 17.2560 Evaluate side-chains 69 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 105 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.033062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.023857 restraints weight = 141031.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.024504 restraints weight = 88145.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.025009 restraints weight = 65172.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.025298 restraints weight = 54354.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025571 restraints weight = 47423.651| |-----------------------------------------------------------------------------| r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15092 Z= 0.195 Angle : 0.565 7.510 20482 Z= 0.308 Chirality : 0.041 0.124 2513 Planarity : 0.003 0.028 2604 Dihedral : 4.689 16.312 2121 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.19), residues: 1946 helix: 1.41 (0.16), residues: 1029 sheet: -0.39 (0.29), residues: 224 loop : -2.23 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 131 TYR 0.007 0.001 TYR G 194 PHE 0.015 0.002 PHE F 261 TRP 0.014 0.002 TRP C 16 Details of bonding type rmsd covalent geometry : bond 0.00389 (15092) covalent geometry : angle 0.56496 (20482) hydrogen bonds : bond 0.04100 ( 995) hydrogen bonds : angle 4.47228 ( 2901) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9561 (ptt) cc_final: 0.9359 (mmm) REVERT: B 47 MET cc_start: 0.9608 (ptp) cc_final: 0.9368 (mmm) REVERT: C 47 MET cc_start: 0.9399 (mmp) cc_final: 0.9178 (mmm) REVERT: D 47 MET cc_start: 0.9611 (ptt) cc_final: 0.9396 (mmm) REVERT: E 47 MET cc_start: 0.9649 (ptt) cc_final: 0.9427 (mmm) REVERT: F 47 MET cc_start: 0.9414 (mmp) cc_final: 0.9211 (mmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0945 time to fit residues: 13.7044 Evaluate side-chains 66 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 97 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 157 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.033130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.023936 restraints weight = 141243.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.024630 restraints weight = 88914.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.025139 restraints weight = 64754.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025474 restraints weight = 53588.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025690 restraints weight = 46855.229| |-----------------------------------------------------------------------------| r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15092 Z= 0.199 Angle : 0.561 7.344 20482 Z= 0.306 Chirality : 0.040 0.122 2513 Planarity : 0.003 0.025 2604 Dihedral : 4.658 16.998 2121 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1946 helix: 1.45 (0.16), residues: 1029 sheet: -0.14 (0.29), residues: 224 loop : -2.14 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.016 0.001 TYR A 250 PHE 0.015 0.002 PHE C 235 TRP 0.016 0.002 TRP B 16 Details of bonding type rmsd covalent geometry : bond 0.00396 (15092) covalent geometry : angle 0.56138 (20482) hydrogen bonds : bond 0.04013 ( 995) hydrogen bonds : angle 4.40752 ( 2901) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.9606 (ptp) cc_final: 0.9373 (mmm) REVERT: C 47 MET cc_start: 0.9409 (mmp) cc_final: 0.9184 (mmm) REVERT: D 47 MET cc_start: 0.9607 (ptt) cc_final: 0.9406 (mmm) REVERT: D 221 MET cc_start: 0.8783 (pmm) cc_final: 0.8506 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0906 time to fit residues: 14.3082 Evaluate side-chains 67 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 95 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.033933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.024596 restraints weight = 139612.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.025187 restraints weight = 86762.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.025802 restraints weight = 65354.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.026017 restraints weight = 53372.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.026339 restraints weight = 47504.586| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15092 Z= 0.125 Angle : 0.528 6.835 20482 Z= 0.283 Chirality : 0.040 0.155 2513 Planarity : 0.003 0.023 2604 Dihedral : 4.445 17.497 2121 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 1946 helix: 1.71 (0.16), residues: 1022 sheet: 0.34 (0.30), residues: 224 loop : -2.06 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 259 TYR 0.006 0.001 TYR D 250 PHE 0.012 0.001 PHE G 235 TRP 0.014 0.001 TRP B 16 Details of bonding type rmsd covalent geometry : bond 0.00254 (15092) covalent geometry : angle 0.52756 (20482) hydrogen bonds : bond 0.03771 ( 995) hydrogen bonds : angle 4.12083 ( 2901) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9349 (mmp) cc_final: 0.9147 (mmm) REVERT: A 126 MET cc_start: 0.9476 (tmm) cc_final: 0.9273 (ppp) REVERT: A 221 MET cc_start: 0.8833 (pmm) cc_final: 0.8580 (mpp) REVERT: B 1 MET cc_start: 0.7411 (ptp) cc_final: 0.7114 (ptt) REVERT: B 47 MET cc_start: 0.9614 (ptp) cc_final: 0.9409 (mmm) REVERT: B 126 MET cc_start: 0.9505 (tmm) cc_final: 0.9281 (tmm) REVERT: B 221 MET cc_start: 0.8864 (pmm) cc_final: 0.8405 (mpp) REVERT: C 47 MET cc_start: 0.9452 (mmp) cc_final: 0.9228 (mmm) REVERT: C 221 MET cc_start: 0.8800 (pmm) cc_final: 0.8331 (mpp) REVERT: E 221 MET cc_start: 0.8852 (pmm) cc_final: 0.8466 (mpp) REVERT: F 126 MET cc_start: 0.9492 (tmm) cc_final: 0.9207 (ppp) REVERT: F 221 MET cc_start: 0.8952 (pmm) cc_final: 0.8473 (mpp) REVERT: G 221 MET cc_start: 0.8786 (pmm) cc_final: 0.8500 (mpp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0932 time to fit residues: 16.0195 Evaluate side-chains 85 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 166 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN D 210 GLN E 210 GLN F 247 GLN G 210 GLN G 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.033309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.024114 restraints weight = 143059.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.024698 restraints weight = 88828.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.025211 restraints weight = 66899.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.025521 restraints weight = 54319.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025830 restraints weight = 48232.613| |-----------------------------------------------------------------------------| r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15092 Z= 0.175 Angle : 0.542 6.341 20482 Z= 0.294 Chirality : 0.040 0.123 2513 Planarity : 0.003 0.024 2604 Dihedral : 4.506 17.172 2121 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.19), residues: 1946 helix: 1.65 (0.16), residues: 1022 sheet: 0.16 (0.30), residues: 224 loop : -2.02 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 214 TYR 0.008 0.001 TYR C 250 PHE 0.011 0.001 PHE G 235 TRP 0.012 0.001 TRP D 16 Details of bonding type rmsd covalent geometry : bond 0.00351 (15092) covalent geometry : angle 0.54234 (20482) hydrogen bonds : bond 0.03724 ( 995) hydrogen bonds : angle 4.23930 ( 2901) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.9603 (ptp) cc_final: 0.9398 (mmm) REVERT: B 221 MET cc_start: 0.8843 (pmm) cc_final: 0.8412 (mpp) REVERT: C 47 MET cc_start: 0.9445 (mmp) cc_final: 0.9227 (mmm) REVERT: C 257 ILE cc_start: 0.9797 (tt) cc_final: 0.9578 (tt) REVERT: C 260 GLU cc_start: 0.9309 (mp0) cc_final: 0.8754 (mp0) REVERT: D 126 MET cc_start: 0.9533 (tmm) cc_final: 0.9303 (tmm) REVERT: E 47 MET cc_start: 0.9440 (mmp) cc_final: 0.9225 (mmm) REVERT: E 135 TYR cc_start: 0.9560 (t80) cc_final: 0.9315 (t80) REVERT: E 257 ILE cc_start: 0.9802 (mt) cc_final: 0.9601 (mt) REVERT: E 260 GLU cc_start: 0.9270 (mp0) cc_final: 0.8866 (mp0) REVERT: G 221 MET cc_start: 0.8723 (pmm) cc_final: 0.8460 (mpp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0906 time to fit residues: 15.0576 Evaluate side-chains 83 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 187 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 162 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN F 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.034055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.024693 restraints weight = 138535.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.025349 restraints weight = 85317.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025953 restraints weight = 63248.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.026249 restraints weight = 51120.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.026397 restraints weight = 44229.406| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15092 Z= 0.126 Angle : 0.524 6.289 20482 Z= 0.280 Chirality : 0.040 0.173 2513 Planarity : 0.003 0.024 2604 Dihedral : 4.407 17.567 2121 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 1946 helix: 1.71 (0.16), residues: 1022 sheet: 0.34 (0.30), residues: 224 loop : -1.96 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.012 0.001 TYR D 250 PHE 0.011 0.001 PHE C 235 TRP 0.011 0.001 TRP A 16 Details of bonding type rmsd covalent geometry : bond 0.00260 (15092) covalent geometry : angle 0.52440 (20482) hydrogen bonds : bond 0.03650 ( 995) hydrogen bonds : angle 4.09673 ( 2901) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9373 (mmp) cc_final: 0.9164 (mmm) REVERT: B 1 MET cc_start: 0.7441 (ptp) cc_final: 0.7176 (ptt) REVERT: B 126 MET cc_start: 0.9481 (tmm) cc_final: 0.9255 (tmm) REVERT: B 221 MET cc_start: 0.8820 (pmm) cc_final: 0.8420 (mpp) REVERT: B 257 ILE cc_start: 0.9797 (mt) cc_final: 0.9539 (mt) REVERT: B 260 GLU cc_start: 0.9327 (mp0) cc_final: 0.8916 (mp0) REVERT: C 47 MET cc_start: 0.9459 (mmp) cc_final: 0.9239 (mmm) REVERT: C 257 ILE cc_start: 0.9773 (tt) cc_final: 0.9517 (tt) REVERT: C 260 GLU cc_start: 0.9251 (mp0) cc_final: 0.8743 (mp0) REVERT: D 1 MET cc_start: 0.7462 (ptp) cc_final: 0.7015 (ptt) REVERT: E 47 MET cc_start: 0.9448 (mmp) cc_final: 0.9242 (mmm) REVERT: E 135 TYR cc_start: 0.9531 (t80) cc_final: 0.9326 (t80) REVERT: E 257 ILE cc_start: 0.9792 (mt) cc_final: 0.9568 (mt) REVERT: E 260 GLU cc_start: 0.9256 (mp0) cc_final: 0.8864 (mp0) REVERT: F 126 MET cc_start: 0.9494 (tmm) cc_final: 0.9174 (tmm) REVERT: G 126 MET cc_start: 0.9430 (tmm) cc_final: 0.9157 (ppp) REVERT: G 221 MET cc_start: 0.8706 (pmm) cc_final: 0.8461 (mpp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1022 time to fit residues: 17.7854 Evaluate side-chains 87 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 179 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 GLN C 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.033352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.024143 restraints weight = 141040.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.024737 restraints weight = 88563.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025365 restraints weight = 66443.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.025705 restraints weight = 53567.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.025895 restraints weight = 46014.356| |-----------------------------------------------------------------------------| r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15092 Z= 0.171 Angle : 0.540 6.100 20482 Z= 0.291 Chirality : 0.040 0.137 2513 Planarity : 0.003 0.023 2604 Dihedral : 4.544 21.539 2121 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 1946 helix: 1.64 (0.16), residues: 1022 sheet: 0.22 (0.30), residues: 238 loop : -2.02 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 214 TYR 0.013 0.001 TYR G 250 PHE 0.010 0.001 PHE G 268 TRP 0.012 0.001 TRP F 16 Details of bonding type rmsd covalent geometry : bond 0.00345 (15092) covalent geometry : angle 0.53988 (20482) hydrogen bonds : bond 0.03645 ( 995) hydrogen bonds : angle 4.20416 ( 2901) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9375 (mmp) cc_final: 0.9166 (mmm) REVERT: B 126 MET cc_start: 0.9516 (tmm) cc_final: 0.9311 (tmm) REVERT: C 47 MET cc_start: 0.9462 (mmp) cc_final: 0.9241 (mmm) REVERT: D 1 MET cc_start: 0.7506 (ptp) cc_final: 0.7210 (ptt) REVERT: D 126 MET cc_start: 0.9533 (tmm) cc_final: 0.9311 (tmm) REVERT: E 47 MET cc_start: 0.9454 (mmp) cc_final: 0.9252 (mmm) REVERT: E 135 TYR cc_start: 0.9556 (t80) cc_final: 0.9246 (t80) REVERT: E 257 ILE cc_start: 0.9789 (mt) cc_final: 0.9569 (mt) REVERT: E 260 GLU cc_start: 0.9261 (mp0) cc_final: 0.8850 (mp0) REVERT: F 126 MET cc_start: 0.9519 (tmm) cc_final: 0.9231 (tmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1031 time to fit residues: 17.8032 Evaluate side-chains 83 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 191 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.034190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.024889 restraints weight = 138885.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025598 restraints weight = 85070.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.026121 restraints weight = 61838.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.026485 restraints weight = 50744.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.026803 restraints weight = 43489.382| |-----------------------------------------------------------------------------| r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15092 Z= 0.113 Angle : 0.538 6.811 20482 Z= 0.281 Chirality : 0.040 0.134 2513 Planarity : 0.003 0.023 2604 Dihedral : 4.429 23.658 2121 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.19), residues: 1946 helix: 1.75 (0.16), residues: 1022 sheet: 0.37 (0.31), residues: 224 loop : -1.95 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.012 0.001 TYR E 250 PHE 0.009 0.001 PHE G 268 TRP 0.007 0.001 TRP G 16 Details of bonding type rmsd covalent geometry : bond 0.00233 (15092) covalent geometry : angle 0.53809 (20482) hydrogen bonds : bond 0.03554 ( 995) hydrogen bonds : angle 3.99398 ( 2901) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7431 (ptt) cc_final: 0.7140 (ptt) REVERT: A 47 MET cc_start: 0.9387 (mmp) cc_final: 0.9170 (mmm) REVERT: A 126 MET cc_start: 0.9491 (tmm) cc_final: 0.9276 (ppp) REVERT: B 47 MET cc_start: 0.9368 (mmp) cc_final: 0.9168 (mmm) REVERT: B 126 MET cc_start: 0.9470 (tmm) cc_final: 0.9240 (tmm) REVERT: C 47 MET cc_start: 0.9483 (mmp) cc_final: 0.9266 (mmm) REVERT: C 126 MET cc_start: 0.9464 (tmm) cc_final: 0.9202 (ppp) REVERT: C 273 MET cc_start: 0.5306 (ptt) cc_final: 0.4973 (ptt) REVERT: D 1 MET cc_start: 0.7334 (ptp) cc_final: 0.6973 (ptt) REVERT: D 126 MET cc_start: 0.9489 (tmm) cc_final: 0.9279 (ppp) REVERT: E 126 MET cc_start: 0.9475 (tmm) cc_final: 0.9183 (ppp) REVERT: E 135 TYR cc_start: 0.9539 (t80) cc_final: 0.9259 (t80) REVERT: F 126 MET cc_start: 0.9496 (tmm) cc_final: 0.9179 (tmm) REVERT: G 126 MET cc_start: 0.9469 (tmm) cc_final: 0.9201 (ppp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0941 time to fit residues: 16.0412 Evaluate side-chains 88 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 193 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.032787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.023955 restraints weight = 144815.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.024591 restraints weight = 88282.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.025161 restraints weight = 65224.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.025447 restraints weight = 52806.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025684 restraints weight = 45954.056| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15092 Z= 0.217 Angle : 0.574 8.392 20482 Z= 0.311 Chirality : 0.040 0.130 2513 Planarity : 0.003 0.024 2604 Dihedral : 4.675 20.523 2121 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.19), residues: 1946 helix: 1.60 (0.16), residues: 1022 sheet: -0.14 (0.29), residues: 224 loop : -1.94 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 256 TYR 0.014 0.001 TYR F 250 PHE 0.010 0.001 PHE G 268 TRP 0.009 0.002 TRP G 16 Details of bonding type rmsd covalent geometry : bond 0.00434 (15092) covalent geometry : angle 0.57359 (20482) hydrogen bonds : bond 0.03721 ( 995) hydrogen bonds : angle 4.28226 ( 2901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.80 seconds wall clock time: 33 minutes 21.54 seconds (2001.54 seconds total)