Starting phenix.real_space_refine on Wed Jul 30 19:46:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s92_40235/07_2025/8s92_40235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s92_40235/07_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_40235/07_2025/8s92_40235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s92_40235/07_2025/8s92_40235.map" model { file = "/net/cci-nas-00/data/ceres_data/8s92_40235/07_2025/8s92_40235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s92_40235/07_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-5711/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: 8.13, per 1000 atoms: 0.64 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: 2.91 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: 1.61 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: 3.16 Time building geometry restraints manager: 3.49 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: 19.910 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 30.230 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.330 ------------------------------------------------------------------------------- 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 : 1.610 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: 0.2649 time to fit residues: 87.6205 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 : 1.499 ------------------------------------------------------------------------------- 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 = 0.159084 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 = 17180.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122760 restraints weight = 15379.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124203 restraints weight = 13849.270| |-----------------------------------------------------------------------------| 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 : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8752 (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: 0.2227 time to fit residues: 77.0222 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 : 1.890 ------------------------------------------------------------------------------- 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: 2.9990 chunk 131 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0010 chunk 151 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.156441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119454 restraints weight = 17374.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117270 restraints weight = 15874.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118748 restraints weight = 18803.448| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1111 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= 0.135 Angle : 0.577 7.259 17523 Z= 0.305 Chirality : 0.044 0.151 2013 Planarity : 0.005 0.075 2235 Dihedral : 4.317 22.412 1719 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.93 % Favored : 84.68 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -2.15 (0.22), residues: 1554 helix: 2.24 (0.28), residues: 360 sheet: -2.39 (0.29), residues: 315 loop : -2.80 (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 0.015 0.001 PHE E 13 TYR 0.012 0.001 TYR D 38 ARG 0.002 0.000 ARG C 270 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 332) hydrogen bonds : angle 4.31515 ( 933) covalent geometry : bond 0.00320 (12954) covalent geometry : angle 0.57747 (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 243 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 LYS cc_start: 0.8779 (mptt) cc_final: 0.8375 (mptt) REVERT: D 201 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8160 (mm-30) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2393 time to fit residues: 85.7378 Evaluate side-chains 175 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121846 restraints weight = 17198.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119374 restraints weight = 23704.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121511 restraints weight = 23290.278| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12954 Z= 0.156 Angle : 0.598 6.265 17523 Z= 0.316 Chirality : 0.045 0.180 2013 Planarity : 0.005 0.075 2235 Dihedral : 4.495 23.075 1719 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.09 % Favored : 85.52 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: -2.25 (0.22), residues: 1554 helix: 2.16 (0.28), residues: 360 sheet: -2.51 (0.28), residues: 315 loop : -2.83 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 288 HIS 0.014 0.001 HIS F 37 PHE 0.014 0.001 PHE C 251 TYR 0.011 0.001 TYR F 20 ARG 0.003 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 332) hydrogen bonds : angle 4.26546 ( 933) covalent geometry : bond 0.00370 (12954) covalent geometry : angle 0.59795 (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 235 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8695 (mp10) cc_final: 0.8456 (mp10) REVERT: A 295 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 93 LYS cc_start: 0.8856 (mptt) cc_final: 0.8520 (mptt) REVERT: D 201 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8141 (mm-30) REVERT: D 209 GLN cc_start: 0.8333 (tt0) cc_final: 0.8068 (tt0) REVERT: C 97 GLN cc_start: 0.8793 (mp10) cc_final: 0.8533 (mp10) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2203 time to fit residues: 77.3283 Evaluate side-chains 185 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 109 optimal weight: 0.1980 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS C 360 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120213 restraints weight = 17329.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118596 restraints weight = 20082.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119571 restraints weight = 23560.304| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12954 Z= 0.123 Angle : 0.571 5.651 17523 Z= 0.302 Chirality : 0.044 0.175 2013 Planarity : 0.005 0.071 2235 Dihedral : 4.374 22.619 1719 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.77 % Favored : 85.84 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.25 (0.22), residues: 1554 helix: 2.12 (0.28), residues: 360 sheet: -2.58 (0.27), residues: 321 loop : -2.79 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 248 HIS 0.011 0.001 HIS D 37 PHE 0.017 0.001 PHE E 13 TYR 0.010 0.001 TYR D 38 ARG 0.003 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 332) hydrogen bonds : angle 4.21375 ( 933) covalent geometry : bond 0.00284 (12954) covalent geometry : angle 0.57115 (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 240 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 LYS cc_start: 0.8827 (mptt) cc_final: 0.8457 (mptt) REVERT: D 201 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8133 (mm-30) REVERT: D 209 GLN cc_start: 0.8312 (tt0) cc_final: 0.8036 (tt0) REVERT: B 295 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7440 (tm-30) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2228 time to fit residues: 78.7862 Evaluate side-chains 188 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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: 0.0020 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 148 optimal weight: 0.0170 chunk 89 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7430 ------------------------------------------------------------------------------- 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 37 HIS D 152 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125091 restraints weight = 17044.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123857 restraints weight = 22595.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124643 restraints weight = 24449.614| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12954 Z= 0.123 Angle : 0.578 5.914 17523 Z= 0.304 Chirality : 0.044 0.207 2013 Planarity : 0.005 0.070 2235 Dihedral : 4.339 22.594 1719 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.64 % Favored : 85.97 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: 2.15 (0.28), residues: 360 sheet: -2.57 (0.27), residues: 321 loop : -2.79 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 248 HIS 0.009 0.001 HIS F 37 PHE 0.018 0.001 PHE C 251 TYR 0.013 0.001 TYR F 145 ARG 0.003 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 332) hydrogen bonds : angle 4.18160 ( 933) covalent geometry : bond 0.00287 (12954) covalent geometry : angle 0.57765 (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 243 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7539 (tm-30) REVERT: D 93 LYS cc_start: 0.8858 (mptt) cc_final: 0.8530 (mptt) REVERT: D 201 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8161 (mm-30) REVERT: E 218 ARG cc_start: 0.7631 (ptt90) cc_final: 0.7414 (ptt90) REVERT: C 97 GLN cc_start: 0.8740 (mp10) cc_final: 0.8422 (mp10) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2252 time to fit residues: 80.9911 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 : 1.462 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 87 optimal weight: 0.0040 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 59 optimal weight: 0.2980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126686 restraints weight = 16904.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124614 restraints weight = 21817.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127117 restraints weight = 19952.584| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12954 Z= 0.109 Angle : 0.581 8.770 17523 Z= 0.304 Chirality : 0.044 0.227 2013 Planarity : 0.005 0.069 2235 Dihedral : 4.287 26.524 1719 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.81 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: -2.20 (0.22), residues: 1554 helix: 2.13 (0.28), residues: 360 sheet: -2.49 (0.27), residues: 321 loop : -2.77 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 248 HIS 0.016 0.001 HIS D 37 PHE 0.012 0.001 PHE E 13 TYR 0.011 0.001 TYR D 38 ARG 0.004 0.000 ARG E 111 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 332) hydrogen bonds : angle 4.15934 ( 933) covalent geometry : bond 0.00246 (12954) covalent geometry : angle 0.58054 (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 257 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 LYS cc_start: 0.8738 (mptt) cc_final: 0.8410 (mptt) REVERT: D 201 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 97 GLN cc_start: 0.8631 (mp10) cc_final: 0.8332 (mp10) REVERT: B 295 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7325 (tm-30) REVERT: C 97 GLN cc_start: 0.8780 (mp10) cc_final: 0.8568 (mp10) REVERT: F 131 ILE cc_start: 0.9467 (mm) cc_final: 0.9248 (mt) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2255 time to fit residues: 86.0389 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 : 1.548 ------------------------------------------------------------------------------- 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: 1.9990 chunk 111 optimal weight: 0.0370 chunk 119 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7878 ------------------------------------------------------------------------------- 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 37 HIS D 152 HIS ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121867 restraints weight = 17616.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118712 restraints weight = 19010.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120698 restraints weight = 18382.061| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12954 Z= 0.127 Angle : 0.593 6.063 17523 Z= 0.312 Chirality : 0.045 0.241 2013 Planarity : 0.005 0.069 2235 Dihedral : 4.309 22.909 1719 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.96 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -2.23 (0.22), residues: 1554 helix: 2.08 (0.28), residues: 360 sheet: -2.49 (0.27), residues: 321 loop : -2.78 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 288 HIS 0.009 0.001 HIS F 37 PHE 0.019 0.001 PHE C 251 TYR 0.012 0.001 TYR F 145 ARG 0.003 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 332) hydrogen bonds : angle 4.20315 ( 933) covalent geometry : bond 0.00298 (12954) covalent geometry : angle 0.59286 (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 238 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7341 (tm-30) REVERT: D 93 LYS cc_start: 0.8798 (mptt) cc_final: 0.8462 (mptt) REVERT: D 201 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8140 (mm-30) REVERT: E 35 ASP cc_start: 0.8334 (p0) cc_final: 0.7870 (p0) REVERT: E 218 ARG cc_start: 0.7483 (ptt90) cc_final: 0.7250 (ptt90) REVERT: C 97 GLN cc_start: 0.8886 (mp10) cc_final: 0.8620 (mp10) REVERT: F 220 MET cc_start: 0.8401 (ttm) cc_final: 0.8172 (ttm) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2133 time to fit residues: 76.5705 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 : 1.460 ------------------------------------------------------------------------------- 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: 4.9990 chunk 137 optimal weight: 0.0060 chunk 9 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 overall best weight: 0.3834 ------------------------------------------------------------------------------- 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 C 213 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124963 restraints weight = 17050.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122498 restraints weight = 19248.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124006 restraints weight = 22257.060| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12954 Z= 0.104 Angle : 0.585 5.808 17523 Z= 0.306 Chirality : 0.044 0.225 2013 Planarity : 0.005 0.068 2235 Dihedral : 4.212 24.225 1719 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.97 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -2.14 (0.22), residues: 1554 helix: 2.12 (0.28), residues: 360 sheet: -2.34 (0.27), residues: 321 loop : -2.74 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 248 HIS 0.020 0.001 HIS D 37 PHE 0.021 0.001 PHE E 13 TYR 0.013 0.001 TYR D 38 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 332) hydrogen bonds : angle 4.10392 ( 933) covalent geometry : bond 0.00232 (12954) covalent geometry : angle 0.58532 (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 243 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7521 (tm-30) REVERT: D 22 LYS cc_start: 0.8305 (pptt) cc_final: 0.7975 (tppt) REVERT: D 93 LYS cc_start: 0.8728 (mptt) cc_final: 0.8397 (mptt) REVERT: D 201 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8116 (mm-30) REVERT: B 97 GLN cc_start: 0.8729 (mp10) cc_final: 0.8397 (mp10) REVERT: B 295 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7328 (tm-30) REVERT: E 218 ARG cc_start: 0.7483 (ptt90) cc_final: 0.7277 (ptt90) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2148 time to fit residues: 78.4197 Evaluate side-chains 192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 137 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 F 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127229 restraints weight = 16761.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125534 restraints weight = 22742.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126492 restraints weight = 24034.230| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12954 Z= 0.112 Angle : 0.592 8.963 17523 Z= 0.309 Chirality : 0.045 0.213 2013 Planarity : 0.005 0.068 2235 Dihedral : 4.210 23.677 1719 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.19 % Favored : 86.36 % 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: -2.12 (0.22), residues: 1554 helix: 2.11 (0.28), residues: 360 sheet: -2.36 (0.27), residues: 321 loop : -2.71 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 248 HIS 0.008 0.001 HIS E 37 PHE 0.020 0.001 PHE E 13 TYR 0.014 0.001 TYR D 20 ARG 0.004 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.03107 ( 332) hydrogen bonds : angle 4.12574 ( 933) covalent geometry : bond 0.00255 (12954) covalent geometry : angle 0.59174 (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 235 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 22 LYS cc_start: 0.8291 (pptt) cc_final: 0.7994 (tppt) REVERT: D 35 ASP cc_start: 0.8552 (p0) cc_final: 0.8306 (p0) REVERT: D 93 LYS cc_start: 0.8721 (mptt) cc_final: 0.8422 (mptt) REVERT: D 201 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B 97 GLN cc_start: 0.8697 (mp10) cc_final: 0.8359 (mp10) REVERT: B 295 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 296 LEU cc_start: 0.7894 (tp) cc_final: 0.7543 (tp) REVERT: E 35 ASP cc_start: 0.8273 (p0) cc_final: 0.7979 (p0) REVERT: E 218 ARG cc_start: 0.7588 (ptt90) cc_final: 0.7380 (ptt90) REVERT: C 97 GLN cc_start: 0.8760 (mp10) cc_final: 0.8467 (mp10) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2256 time to fit residues: 79.3115 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 : 1.540 ------------------------------------------------------------------------------- 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: 0.0070 chunk 151 optimal weight: 0.1980 chunk 82 optimal weight: 0.2980 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 119 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 overall best weight: 0.1976 ------------------------------------------------------------------------------- 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 ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121819 restraints weight = 17591.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119383 restraints weight = 16213.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120961 restraints weight = 19838.401| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2176 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= 0.101 Angle : 0.592 10.907 17523 Z= 0.307 Chirality : 0.044 0.187 2013 Planarity : 0.005 0.067 2235 Dihedral : 4.189 27.585 1719 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.75 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -2.05 (0.22), residues: 1554 helix: 2.08 (0.28), residues: 360 sheet: -2.21 (0.27), residues: 321 loop : -2.66 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 248 HIS 0.027 0.001 HIS F 37 PHE 0.018 0.001 PHE E 13 TYR 0.021 0.001 TYR A 258 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.02619 ( 332) hydrogen bonds : angle 3.99284 ( 933) covalent geometry : bond 0.00219 (12954) covalent geometry : angle 0.59155 (17523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4039.81 seconds wall clock time: 72 minutes 53.20 seconds (4373.20 seconds total)