Starting phenix.real_space_refine on Thu May 15 04:38:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s92_40235/05_2025/8s92_40235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s92_40235/05_2025/8s92_40235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s92_40235/05_2025/8s92_40235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s92_40235/05_2025/8s92_40235.map" model { file = "/net/cci-nas-00/data/ceres_data/8s92_40235/05_2025/8s92_40235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s92_40235/05_2025/8s92_40235.cif" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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 96 5.16 5 C 8079 2.51 5 N 2139 2.21 5 O 2400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2168 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 15, 'TRANS': 258} Chain breaks: 2 Chain: "D" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2070 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Chain breaks: 2 Chain: "B" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2168 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 15, 'TRANS': 258} Chain breaks: 2 Chain: "E" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2070 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Chain breaks: 2 Chain: "C" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2168 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 15, 'TRANS': 258} Chain breaks: 2 Chain: "F" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2070 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Chain breaks: 2 Time building chain proxies: 8.21, per 1000 atoms: 0.65 Number of scatterers: 12714 At special positions: 0 Unit cell: (142.08, 153.18, 78.81, 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 96 16.00 O 2400 8.00 N 2139 7.00 C 8079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.7 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 18 sheets defined 28.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.655A pdb=" N TRP A 78 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 79' Processing helix chain 'A' and resid 91 through 106 removed outlier: 4.153A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.644A pdb=" N ILE A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.637A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.772A pdb=" N CYS A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.888A pdb=" N VAL D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 7 " --> pdb=" O SER D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.775A pdb=" N ILE D 25 " --> pdb=" O HIS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 removed outlier: 3.523A pdb=" N ASN D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 63 through 83 removed outlier: 4.026A pdb=" N THR D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.777A pdb=" N GLN D 162 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 163 " --> pdb=" O PHE D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.635A pdb=" N TRP B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS B 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 75 through 79' Processing helix chain 'B' and resid 91 through 106 removed outlier: 4.200A pdb=" N LYS B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.647A pdb=" N ILE B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.643A pdb=" N ILE B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 150 through 175 removed outlier: 3.732A pdb=" N CYS B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.872A pdb=" N VAL E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 7 " --> pdb=" O SER E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 removed outlier: 3.765A pdb=" N ILE E 25 " --> pdb=" O HIS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 63 through 83 removed outlier: 3.946A pdb=" N THR E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.667A pdb=" N GLN E 162 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR E 163 " --> pdb=" O PHE E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'C' and resid 75 through 79 removed outlier: 3.623A pdb=" N TRP C 78 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 79' Processing helix chain 'C' and resid 91 through 106 removed outlier: 4.179A pdb=" N LYS C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.642A pdb=" N ILE C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 132 through 138 removed outlier: 3.633A pdb=" N ILE C 138 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 150 through 175 removed outlier: 3.770A pdb=" N CYS C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.864A pdb=" N VAL F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR F 7 " --> pdb=" O SER F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.807A pdb=" N ILE F 25 " --> pdb=" O HIS F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 63 through 83 removed outlier: 3.985A pdb=" N THR F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.804A pdb=" N GLN F 162 " --> pdb=" O ASP F 159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR F 163 " --> pdb=" O PHE F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 225 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.445A pdb=" N ARG A 197 " --> pdb=" O VAL A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220 removed outlier: 3.688A pdb=" N ILE A 219 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 333 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 332 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR A 310 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ILE A 357 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU A 312 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA A 359 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU A 314 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N SER A 361 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 311 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 294 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 224 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA4, first strand: chain 'D' and resid 38 through 39 removed outlier: 7.239A pdb=" N TYR D 38 " --> pdb=" O HIS D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 42 through 43 removed outlier: 6.360A pdb=" N VAL D 42 " --> pdb=" O SER D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 238 through 240 removed outlier: 3.613A pdb=" N GLY D 128 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS D 203 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR D 133 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU D 201 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 224 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N SER D 219 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LEU D 263 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS D 221 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA D 265 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE D 223 " --> pdb=" O ALA D 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.437A pdb=" N ARG B 197 " --> pdb=" O VAL B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.702A pdb=" N ILE B 219 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 333 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 332 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR B 310 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ILE B 357 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU B 312 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA B 359 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU B 314 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N SER B 361 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 311 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 294 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 224 " --> pdb=" O GLN B 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB1, first strand: chain 'E' and resid 38 through 39 removed outlier: 7.219A pdb=" N TYR E 38 " --> pdb=" O HIS E 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 43 removed outlier: 6.320A pdb=" N VAL E 42 " --> pdb=" O SER E 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 238 through 240 removed outlier: 3.736A pdb=" N GLY E 128 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS E 203 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR E 133 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU E 201 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN E 200 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 224 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N SER E 219 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N LEU E 263 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ALA E 265 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE E 223 " --> pdb=" O ALA E 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 121 through 124 removed outlier: 6.433A pdb=" N ARG C 197 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 219 through 220 removed outlier: 3.695A pdb=" N ILE C 219 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 333 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR C 332 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR C 310 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N ILE C 357 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU C 312 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA C 359 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU C 314 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER C 361 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 311 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 294 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 224 " --> pdb=" O GLN C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 39 removed outlier: 7.299A pdb=" N TYR F 38 " --> pdb=" O HIS F 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.348A pdb=" N VAL F 42 " --> pdb=" O SER F 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 238 through 240 removed outlier: 3.620A pdb=" N GLY F 128 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS F 203 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR F 133 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU F 201 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 200 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU F 224 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N SER F 219 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LEU F 263 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LYS F 221 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA F 265 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE F 223 " --> pdb=" O ALA F 265 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2771 1.33 - 1.45: 2637 1.45 - 1.57: 7406 1.57 - 1.69: 2 1.69 - 1.81: 138 Bond restraints: 12954 Sorted by residual: bond pdb=" CB PRO D 193 " pdb=" CG PRO D 193 " ideal model delta sigma weight residual 1.492 1.671 -0.179 5.00e-02 4.00e+02 1.28e+01 bond pdb=" CB PRO E 193 " pdb=" CG PRO E 193 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" N PRO D 193 " pdb=" CA PRO D 193 " ideal model delta sigma weight residual 1.466 1.429 0.037 1.50e-02 4.44e+03 6.23e+00 bond pdb=" N PRO E 193 " pdb=" CA PRO E 193 " ideal model delta sigma weight residual 1.466 1.434 0.032 1.50e-02 4.44e+03 4.64e+00 bond pdb=" CG PRO E 193 " pdb=" CD PRO E 193 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.47e+00 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 17407 3.16 - 6.33: 104 6.33 - 9.49: 8 9.49 - 12.66: 2 12.66 - 15.82: 2 Bond angle restraints: 17523 Sorted by residual: angle pdb=" CA PRO D 193 " pdb=" N PRO D 193 " pdb=" CD PRO D 193 " ideal model delta sigma weight residual 112.00 96.18 15.82 1.40e+00 5.10e-01 1.28e+02 angle pdb=" CA PRO E 193 " pdb=" N PRO E 193 " pdb=" CD PRO E 193 " ideal model delta sigma weight residual 112.00 96.84 15.16 1.40e+00 5.10e-01 1.17e+02 angle pdb=" N PRO D 193 " pdb=" CD PRO D 193 " pdb=" CG PRO D 193 " ideal model delta sigma weight residual 103.20 93.51 9.69 1.50e+00 4.44e-01 4.17e+01 angle pdb=" N PRO E 193 " pdb=" CD PRO E 193 " pdb=" CG PRO E 193 " ideal model delta sigma weight residual 103.20 93.52 9.68 1.50e+00 4.44e-01 4.17e+01 angle pdb=" CA ARG C 272 " pdb=" CB ARG C 272 " pdb=" CG ARG C 272 " ideal model delta sigma weight residual 114.10 123.31 -9.21 2.00e+00 2.50e-01 2.12e+01 ... (remaining 17518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7063 17.99 - 35.99: 738 35.99 - 53.98: 132 53.98 - 71.97: 11 71.97 - 89.96: 15 Dihedral angle restraints: 7959 sinusoidal: 3264 harmonic: 4695 Sorted by residual: dihedral pdb=" CA ASN F 59 " pdb=" C ASN F 59 " pdb=" N MET F 60 " pdb=" CA MET F 60 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASN D 59 " pdb=" C ASN D 59 " pdb=" N MET D 60 " pdb=" CA MET D 60 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASN E 59 " pdb=" C ASN E 59 " pdb=" N MET E 60 " pdb=" CA MET E 60 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 7956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1349 0.035 - 0.070: 383 0.070 - 0.105: 202 0.105 - 0.139: 73 0.139 - 0.174: 6 Chirality restraints: 2013 Sorted by residual: chirality pdb=" CA ARG C 272 " pdb=" N ARG C 272 " pdb=" C ARG C 272 " pdb=" CB ARG C 272 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA GLN A 97 " pdb=" N GLN A 97 " pdb=" C GLN A 97 " pdb=" CB GLN A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CB ILE B 138 " pdb=" CA ILE B 138 " pdb=" CG1 ILE B 138 " pdb=" CG2 ILE B 138 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 2010 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 61 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO D 62 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO D 62 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 62 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 266 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 267 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 266 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO C 267 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 267 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 267 " 0.043 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 86 2.61 - 3.19: 10831 3.19 - 3.76: 17119 3.76 - 4.33: 21651 4.33 - 4.90: 36162 Nonbonded interactions: 85849 Sorted by model distance: nonbonded pdb=" O ALA F 36 " pdb=" ND1 HIS F 37 " model vdw 2.043 3.120 nonbonded pdb=" NZ LYS C 336 " pdb=" OE1 GLU C 358 " model vdw 2.334 3.120 nonbonded pdb=" O ILE A 93 " pdb=" OE1 GLN A 97 " model vdw 2.336 3.040 nonbonded pdb=" NZ LYS B 336 " pdb=" OE1 GLU B 358 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS A 336 " pdb=" OE1 GLU A 358 " model vdw 2.358 3.120 ... (remaining 85844 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.720 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 29.650 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.004 0.179 12954 Z= 0.141 Angle : 0.676 15.819 17523 Z= 0.382 Chirality : 0.045 0.174 2013 Planarity : 0.006 0.113 2235 Dihedral : 14.722 89.963 4899 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.51 % Favored : 86.10 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.22), residues: 1554 helix: 1.77 (0.28), residues: 363 sheet: -2.18 (0.28), residues: 366 loop : -2.78 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 248 HIS 0.011 0.001 HIS E 37 PHE 0.020 0.001 PHE C 251 TYR 0.014 0.001 TYR E 145 ARG 0.005 0.000 ARG C 272 Details of bonding type rmsd hydrogen bonds : bond 0.18649 ( 332) hydrogen bonds : angle 6.30459 ( 933) covalent geometry : bond 0.00356 (12954) covalent geometry : angle 0.67636 (17523) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2249 time to fit residues: 73.6731 Evaluate side-chains 182 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS D 5 GLN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 162 GLN B 106 HIS E 5 GLN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122750 restraints weight = 17180.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122754 restraints weight = 15380.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124204 restraints weight = 13846.483| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 12954 Z= 0.107 Angle : 0.555 7.387 17523 Z= 0.294 Chirality : 0.043 0.140 2013 Planarity : 0.005 0.078 2235 Dihedral : 4.224 23.096 1719 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.38 % Favored : 86.23 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.22), residues: 1554 helix: 2.14 (0.28), residues: 360 sheet: -2.18 (0.28), residues: 339 loop : -2.89 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 248 HIS 0.007 0.001 HIS E 37 PHE 0.014 0.001 PHE C 251 TYR 0.015 0.001 TYR F 38 ARG 0.002 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 332) hydrogen bonds : angle 4.35733 ( 933) covalent geometry : bond 0.00257 (12954) covalent geometry : angle 0.55524 (17523) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8753 (mp10) cc_final: 0.8316 (mp10) REVERT: E 33 ASP cc_start: 0.8598 (t0) cc_final: 0.8386 (t0) REVERT: C 97 GLN cc_start: 0.8731 (mp10) cc_final: 0.8503 (mp10) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2049 time to fit residues: 70.8100 Evaluate side-chains 183 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.0370 chunk 151 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS B 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119059 restraints weight = 17414.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116741 restraints weight = 15880.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118087 restraints weight = 19359.749| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12954 Z= 0.138 Angle : 0.583 7.269 17523 Z= 0.308 Chirality : 0.044 0.158 2013 Planarity : 0.005 0.075 2235 Dihedral : 4.346 22.391 1719 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.86 % Favored : 84.75 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.22), residues: 1554 helix: 2.22 (0.28), residues: 360 sheet: -2.41 (0.29), residues: 315 loop : -2.81 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 288 HIS 0.009 0.001 HIS F 37 PHE 0.016 0.001 PHE E 13 TYR 0.012 0.001 TYR D 38 ARG 0.002 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 332) hydrogen bonds : angle 4.31127 ( 933) covalent geometry : bond 0.00325 (12954) covalent geometry : angle 0.58264 (17523) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.403 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: A 97 GLN cc_start: 0.8740 (mp10) cc_final: 0.8519 (mp10) REVERT: D 93 LYS cc_start: 0.8807 (mptt) cc_final: 0.8380 (mptt) REVERT: D 201 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8170 (mm-30) REVERT: E 33 ASP cc_start: 0.8789 (t0) cc_final: 0.8564 (t0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2272 time to fit residues: 81.8108 Evaluate side-chains 179 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 84 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.0170 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120979 restraints weight = 17359.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119739 restraints weight = 15153.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121264 restraints weight = 17038.599| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12954 Z= 0.096 Angle : 0.552 6.464 17523 Z= 0.287 Chirality : 0.043 0.160 2013 Planarity : 0.005 0.075 2235 Dihedral : 4.179 24.625 1719 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.78 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1554 helix: 2.32 (0.28), residues: 360 sheet: -2.31 (0.28), residues: 318 loop : -2.78 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 248 HIS 0.010 0.001 HIS E 37 PHE 0.016 0.001 PHE C 251 TYR 0.014 0.001 TYR F 145 ARG 0.002 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 332) hydrogen bonds : angle 3.97187 ( 933) covalent geometry : bond 0.00213 (12954) covalent geometry : angle 0.55180 (17523) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 LYS cc_start: 0.8674 (mptt) cc_final: 0.8271 (mptt) REVERT: D 201 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8187 (mm-30) REVERT: D 209 GLN cc_start: 0.8331 (tt0) cc_final: 0.8074 (tt0) REVERT: C 97 GLN cc_start: 0.8837 (mp10) cc_final: 0.8580 (mp10) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2074 time to fit residues: 76.3042 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.0050 chunk 109 optimal weight: 0.0870 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119284 restraints weight = 17537.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117612 restraints weight = 15249.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119228 restraints weight = 16077.145| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12954 Z= 0.107 Angle : 0.554 6.006 17523 Z= 0.290 Chirality : 0.044 0.173 2013 Planarity : 0.005 0.070 2235 Dihedral : 4.125 22.600 1719 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.26 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.22), residues: 1554 helix: 2.23 (0.28), residues: 360 sheet: -2.35 (0.27), residues: 324 loop : -2.71 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 248 HIS 0.017 0.001 HIS E 37 PHE 0.010 0.001 PHE D 48 TYR 0.009 0.001 TYR D 38 ARG 0.002 0.000 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 332) hydrogen bonds : angle 4.08135 ( 933) covalent geometry : bond 0.00241 (12954) covalent geometry : angle 0.55399 (17523) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8781 (mp10) cc_final: 0.8481 (mp10) REVERT: D 35 ASP cc_start: 0.8546 (p0) cc_final: 0.8270 (p0) REVERT: D 93 LYS cc_start: 0.8718 (mptt) cc_final: 0.8278 (mptt) REVERT: D 201 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8148 (mm-30) REVERT: D 209 GLN cc_start: 0.8346 (tt0) cc_final: 0.8079 (tt0) REVERT: B 97 GLN cc_start: 0.8662 (mp10) cc_final: 0.8404 (mp10) REVERT: E 35 ASP cc_start: 0.8436 (p0) cc_final: 0.8116 (p0) REVERT: F 131 ILE cc_start: 0.9452 (mm) cc_final: 0.9218 (mt) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2344 time to fit residues: 83.3313 Evaluate side-chains 190 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 148 optimal weight: 0.4980 chunk 89 optimal weight: 0.0970 chunk 123 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121901 restraints weight = 17490.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119575 restraints weight = 15375.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121214 restraints weight = 16262.851| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12954 Z= 0.101 Angle : 0.554 5.796 17523 Z= 0.288 Chirality : 0.043 0.187 2013 Planarity : 0.005 0.070 2235 Dihedral : 4.114 23.140 1719 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.10 % Favored : 87.52 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1554 helix: 2.28 (0.28), residues: 360 sheet: -2.24 (0.27), residues: 321 loop : -2.68 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 248 HIS 0.011 0.001 HIS E 37 PHE 0.018 0.001 PHE C 251 TYR 0.013 0.001 TYR F 145 ARG 0.004 0.000 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 332) hydrogen bonds : angle 3.98143 ( 933) covalent geometry : bond 0.00230 (12954) covalent geometry : angle 0.55355 (17523) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8817 (mp10) cc_final: 0.8532 (mp10) REVERT: D 93 LYS cc_start: 0.8743 (mptt) cc_final: 0.8339 (mptt) REVERT: D 201 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8209 (mm-30) REVERT: D 209 GLN cc_start: 0.8357 (tt0) cc_final: 0.8126 (tt0) REVERT: C 97 GLN cc_start: 0.8867 (mp10) cc_final: 0.8509 (mp10) REVERT: C 213 ASN cc_start: 0.8914 (m110) cc_final: 0.8676 (m110) REVERT: F 131 ILE cc_start: 0.9459 (mm) cc_final: 0.9219 (mt) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2348 time to fit residues: 85.2601 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 0.0010 chunk 92 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 5 optimal weight: 0.0470 chunk 87 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 HIS C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121485 restraints weight = 17690.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120462 restraints weight = 16173.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121477 restraints weight = 17876.519| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12954 Z= 0.101 Angle : 0.559 6.379 17523 Z= 0.290 Chirality : 0.044 0.177 2013 Planarity : 0.005 0.069 2235 Dihedral : 4.071 26.492 1719 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.87 % Favored : 86.74 % Rotamer: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1554 helix: 2.28 (0.28), residues: 360 sheet: -2.22 (0.27), residues: 321 loop : -2.65 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 248 HIS 0.010 0.001 HIS E 37 PHE 0.012 0.001 PHE E 13 TYR 0.009 0.001 TYR A 81 ARG 0.006 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 332) hydrogen bonds : angle 3.94520 ( 933) covalent geometry : bond 0.00229 (12954) covalent geometry : angle 0.55899 (17523) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 LYS cc_start: 0.8686 (mptt) cc_final: 0.8333 (mptt) REVERT: D 201 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8237 (mm-30) REVERT: D 209 GLN cc_start: 0.8307 (tt0) cc_final: 0.8034 (tt0) REVERT: B 97 GLN cc_start: 0.8589 (mp10) cc_final: 0.8238 (mp10) REVERT: C 97 GLN cc_start: 0.8828 (mp10) cc_final: 0.8574 (mp10) REVERT: C 213 ASN cc_start: 0.8969 (m110) cc_final: 0.8695 (m110) REVERT: F 131 ILE cc_start: 0.9459 (mm) cc_final: 0.9223 (mt) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.2144 time to fit residues: 75.6715 Evaluate side-chains 194 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123098 restraints weight = 17148.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124376 restraints weight = 29582.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125001 restraints weight = 24799.012| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12954 Z= 0.228 Angle : 0.693 6.133 17523 Z= 0.369 Chirality : 0.048 0.243 2013 Planarity : 0.006 0.069 2235 Dihedral : 4.823 21.569 1719 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.47 % Favored : 83.14 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.21), residues: 1554 helix: 1.81 (0.28), residues: 360 sheet: -2.63 (0.26), residues: 321 loop : -2.75 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 288 HIS 0.010 0.001 HIS E 37 PHE 0.018 0.002 PHE E 13 TYR 0.019 0.002 TYR C 199 ARG 0.005 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 332) hydrogen bonds : angle 4.57999 ( 933) covalent geometry : bond 0.00548 (12954) covalent geometry : angle 0.69293 (17523) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 201 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8379 (mm-30) REVERT: D 209 GLN cc_start: 0.8203 (tt0) cc_final: 0.7963 (tt0) REVERT: E 117 THR cc_start: 0.9580 (t) cc_final: 0.9306 (m) REVERT: C 199 TYR cc_start: 0.7535 (p90) cc_final: 0.7264 (p90) REVERT: F 220 MET cc_start: 0.8562 (ttm) cc_final: 0.8311 (ttm) REVERT: F 254 ASP cc_start: 0.8827 (m-30) cc_final: 0.8502 (m-30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2419 time to fit residues: 78.3774 Evaluate side-chains 180 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 4 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS D 37 HIS D 152 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115749 restraints weight = 17738.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115581 restraints weight = 16883.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115836 restraints weight = 20495.045| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12954 Z= 0.139 Angle : 0.628 6.017 17523 Z= 0.330 Chirality : 0.045 0.219 2013 Planarity : 0.005 0.068 2235 Dihedral : 4.568 23.293 1719 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.71 % Favored : 85.91 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1554 helix: 1.89 (0.28), residues: 360 sheet: -2.57 (0.26), residues: 321 loop : -2.75 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 288 HIS 0.010 0.001 HIS E 37 PHE 0.017 0.001 PHE D 13 TYR 0.020 0.001 TYR C 258 ARG 0.006 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 332) hydrogen bonds : angle 4.40012 ( 933) covalent geometry : bond 0.00324 (12954) covalent geometry : angle 0.62764 (17523) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 327 ASP cc_start: 0.8503 (m-30) cc_final: 0.8272 (m-30) REVERT: D 93 LYS cc_start: 0.8664 (mptt) cc_final: 0.8303 (mptt) REVERT: D 201 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 209 GLN cc_start: 0.8265 (tt0) cc_final: 0.8033 (tt0) REVERT: B 97 GLN cc_start: 0.8667 (mp10) cc_final: 0.8229 (mp10) REVERT: C 97 GLN cc_start: 0.8823 (mp10) cc_final: 0.8431 (mp10) REVERT: C 213 ASN cc_start: 0.9016 (m110) cc_final: 0.8711 (m110) REVERT: F 254 ASP cc_start: 0.8901 (m-30) cc_final: 0.8517 (m-30) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2123 time to fit residues: 76.6598 Evaluate side-chains 195 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 151 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS D 152 HIS B 106 HIS C 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115444 restraints weight = 17566.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113841 restraints weight = 18504.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115263 restraints weight = 18383.598| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12954 Z= 0.150 Angle : 0.634 7.915 17523 Z= 0.334 Chirality : 0.046 0.224 2013 Planarity : 0.005 0.069 2235 Dihedral : 4.608 25.909 1719 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.19 % Favored : 84.43 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.21), residues: 1554 helix: 1.85 (0.28), residues: 360 sheet: -2.62 (0.26), residues: 321 loop : -2.75 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 288 HIS 0.018 0.001 HIS D 37 PHE 0.018 0.002 PHE C 251 TYR 0.018 0.001 TYR C 258 ARG 0.006 0.001 ARG C 227 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 332) hydrogen bonds : angle 4.42240 ( 933) covalent geometry : bond 0.00353 (12954) covalent geometry : angle 0.63368 (17523) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8848 (mp10) cc_final: 0.8610 (mp10) REVERT: A 295 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 93 LYS cc_start: 0.8667 (mptt) cc_final: 0.8271 (mptt) REVERT: D 201 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8237 (mm-30) REVERT: D 209 GLN cc_start: 0.8309 (tt0) cc_final: 0.8068 (tt0) REVERT: B 97 GLN cc_start: 0.8684 (mp10) cc_final: 0.8122 (mp10) REVERT: C 97 GLN cc_start: 0.8837 (mp10) cc_final: 0.8347 (mp10) REVERT: F 254 ASP cc_start: 0.8921 (m-30) cc_final: 0.8500 (m-30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2201 time to fit residues: 72.4548 Evaluate side-chains 191 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 19 optimal weight: 0.2980 chunk 151 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 213 ASN D 152 HIS B 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119216 restraints weight = 17418.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117948 restraints weight = 15993.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119192 restraints weight = 16823.994| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12954 Z= 0.108 Angle : 0.600 7.423 17523 Z= 0.314 Chirality : 0.045 0.198 2013 Planarity : 0.005 0.069 2235 Dihedral : 4.396 24.146 1719 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.55 % Favored : 87.07 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.22), residues: 1554 helix: 1.93 (0.28), residues: 360 sheet: -2.46 (0.26), residues: 321 loop : -2.70 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 248 HIS 0.015 0.001 HIS F 37 PHE 0.014 0.001 PHE D 13 TYR 0.020 0.001 TYR A 258 ARG 0.007 0.000 ARG C 227 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 332) hydrogen bonds : angle 4.17636 ( 933) covalent geometry : bond 0.00244 (12954) covalent geometry : angle 0.60006 (17523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.15 seconds wall clock time: 63 minutes 39.54 seconds (3819.54 seconds total)