Starting phenix.real_space_refine on Sat Jul 20 09:56:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/07_2024/8wbc_37420_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/07_2024/8wbc_37420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/07_2024/8wbc_37420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/07_2024/8wbc_37420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/07_2024/8wbc_37420_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/07_2024/8wbc_37420_neut.cif" } resolution = 3.03 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= 0.136 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 84 5.16 5 C 6652 2.51 5 N 1816 2.21 5 O 1997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "a" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2589 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 313} Chain breaks: 1 Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2589 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 313} Chain breaks: 1 Chain: "b" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2589 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 313} Chain breaks: 1 Time building chain proxies: 6.01, per 1000 atoms: 0.57 Number of scatterers: 10549 At special positions: 0 Unit cell: (89.25, 115.6, 117.3, 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 84 16.00 O 1997 8.00 N 1816 7.00 C 6652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.04 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 18.7% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.594A pdb=" N ILE A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASN A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.531A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.544A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.934A pdb=" N LEU A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 271 " --> pdb=" O TRP A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 271' Processing helix chain 'a' and resid 38 through 53 removed outlier: 3.578A pdb=" N ALA a 43 " --> pdb=" O PRO a 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER a 44 " --> pdb=" O ALA a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.884A pdb=" N ASN a 73 " --> pdb=" O LYS a 69 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU a 74 " --> pdb=" O GLN a 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY a 82 " --> pdb=" O VAL a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.731A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 241 removed outlier: 3.880A pdb=" N MET a 241 " --> pdb=" O GLU a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.671A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.505A pdb=" N LEU a 270 " --> pdb=" O PRO a 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 271' Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.871A pdb=" N ASN a 344 " --> pdb=" O LYS a 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.770A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.801A pdb=" N LEU B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.579A pdb=" N HIS B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.854A pdb=" N MET B 241 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.580A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 271 " --> pdb=" O TRP B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 271' Processing helix chain 'b' and resid 38 through 51 removed outlier: 4.065A pdb=" N GLU b 51 " --> pdb=" O LEU b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 82 removed outlier: 3.542A pdb=" N ASN b 65 " --> pdb=" O THR b 61 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE b 66 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN b 73 " --> pdb=" O LYS b 69 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU b 74 " --> pdb=" O GLN b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 146 No H-bonds generated for 'chain 'b' and resid 144 through 146' Processing helix chain 'b' and resid 180 through 183 removed outlier: 4.152A pdb=" N LEU b 183 " --> pdb=" O ASP b 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 180 through 183' Processing helix chain 'b' and resid 226 through 230 removed outlier: 3.934A pdb=" N THR b 230 " --> pdb=" O LYS b 227 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 241 removed outlier: 3.940A pdb=" N MET b 241 " --> pdb=" O GLU b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'b' and resid 267 through 271 removed outlier: 3.680A pdb=" N LEU b 270 " --> pdb=" O PRO b 267 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY b 271 " --> pdb=" O TRP b 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 267 through 271' Processing helix chain 'b' and resid 341 through 345 removed outlier: 3.544A pdb=" N ASN b 344 " --> pdb=" O LYS b 341 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET b 345 " --> pdb=" O GLU b 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 341 through 345' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 3.687A pdb=" N GLY A 16 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.539A pdb=" N ILE A 167 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS A 170 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A 155 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.906A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.496A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER a 205 " --> pdb=" O ILE a 212 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ILE a 212 " --> pdb=" O SER a 205 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU a 274 " --> pdb=" O LEU a 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 removed outlier: 5.991A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 87 through 90 removed outlier: 7.167A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 153 through 157 removed outlier: 6.543A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 284 through 287 Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 16 removed outlier: 3.743A pdb=" N LYS B 14 " --> pdb=" O ALA B 5 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 5 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 16 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B 3 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER b 7 " --> pdb=" O GLU b 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU b 12 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AB2, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.484A pdb=" N LYS B 33 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET B 169 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLN B 35 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N PHE B 171 " --> pdb=" O GLN B 35 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN B 166 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR B 158 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.084A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE B 135 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 89 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 57 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.679A pdb=" N GLU B 274 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE B 212 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER b 185 " --> pdb=" O ALA b 196 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE b 202 " --> pdb=" O HIS b 195 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE b 212 " --> pdb=" O SER b 205 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.042A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 35 through 36 removed outlier: 7.136A pdb=" N GLN b 35 " --> pdb=" O MET b 169 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N PHE b 171 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 87 through 90 removed outlier: 6.504A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 284 through 287 removed outlier: 5.954A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 687 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: 3.17 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1766 1.32 - 1.45: 3028 1.45 - 1.57: 5907 1.57 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 10821 Sorted by residual: bond pdb=" C ILE A 135 " pdb=" O ILE A 135 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.19e-02 7.06e+03 1.49e+01 bond pdb=" C ASP A 136 " pdb=" O ASP A 136 " ideal model delta sigma weight residual 1.235 1.198 0.038 1.26e-02 6.30e+03 8.90e+00 bond pdb=" CA ASP A 136 " pdb=" CB ASP A 136 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.69e-02 3.50e+03 8.83e+00 bond pdb=" CA ILE A 135 " pdb=" C ILE A 135 " ideal model delta sigma weight residual 1.524 1.492 0.031 1.14e-02 7.69e+03 7.47e+00 bond pdb=" CA ASP A 136 " pdb=" C ASP A 136 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.15e+00 ... (remaining 10816 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 377 106.95 - 113.71: 5975 113.71 - 120.48: 3766 120.48 - 127.24: 4364 127.24 - 134.01: 196 Bond angle restraints: 14678 Sorted by residual: angle pdb=" N SER a 9 " pdb=" CA SER a 9 " pdb=" C SER a 9 " ideal model delta sigma weight residual 114.64 109.58 5.06 1.52e+00 4.33e-01 1.11e+01 angle pdb=" C ILE A 135 " pdb=" CA ILE A 135 " pdb=" CB ILE A 135 " ideal model delta sigma weight residual 111.32 107.49 3.83 1.21e+00 6.83e-01 1.00e+01 angle pdb=" N CYS A 4 " pdb=" CA CYS A 4 " pdb=" C CYS A 4 " ideal model delta sigma weight residual 108.42 112.75 -4.33 1.54e+00 4.22e-01 7.89e+00 angle pdb=" N GLY a 161 " pdb=" CA GLY a 161 " pdb=" C GLY a 161 " ideal model delta sigma weight residual 113.18 119.18 -6.00 2.37e+00 1.78e-01 6.40e+00 angle pdb=" CA CYS A 4 " pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " ideal model delta sigma weight residual 114.40 120.21 -5.81 2.30e+00 1.89e-01 6.37e+00 ... (remaining 14673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5893 17.95 - 35.91: 435 35.91 - 53.86: 71 53.86 - 71.81: 18 71.81 - 89.76: 15 Dihedral angle restraints: 6432 sinusoidal: 2615 harmonic: 3817 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 -177.24 -89.76 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 316 " pdb=" CB CYS B 316 " ideal model delta sinusoidal sigma weight residual -86.00 -173.20 87.20 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 143 " pdb=" CB CYS A 143 " ideal model delta sinusoidal sigma weight residual -86.00 -171.78 85.78 1 1.00e+01 1.00e-02 8.89e+01 ... (remaining 6429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1132 0.041 - 0.082: 324 0.082 - 0.124: 104 0.124 - 0.165: 6 0.165 - 0.206: 1 Chirality restraints: 1567 Sorted by residual: chirality pdb=" CA ASP A 136 " pdb=" N ASP A 136 " pdb=" C ASP A 136 " pdb=" CB ASP A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR A 209 " pdb=" CA THR A 209 " pdb=" OG1 THR A 209 " pdb=" CG2 THR A 209 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA CYS A 4 " pdb=" N CYS A 4 " pdb=" C CYS A 4 " pdb=" CB CYS A 4 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1564 not shown) Planarity restraints: 1877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY a 137 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO a 138 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO a 138 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO a 138 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 35 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO A 36 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 208 " 0.005 2.00e-02 2.50e+03 9.85e-03 9.70e-01 pdb=" C GLN A 208 " -0.017 2.00e-02 2.50e+03 pdb=" O GLN A 208 " 0.006 2.00e-02 2.50e+03 pdb=" N THR A 209 " 0.006 2.00e-02 2.50e+03 ... (remaining 1874 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 202 2.68 - 3.24: 9317 3.24 - 3.79: 15160 3.79 - 4.35: 21486 4.35 - 4.90: 36562 Nonbonded interactions: 82727 Sorted by model distance: nonbonded pdb=" OH TYR a 158 " pdb=" O ARG a 182 " model vdw 2.129 2.440 nonbonded pdb=" OG SER B 297 " pdb=" O TYR B 331 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR B 283 " pdb=" OH TYR B 331 " model vdw 2.244 2.440 nonbonded pdb=" O TRP a 68 " pdb=" OG1 THR a 72 " model vdw 2.260 2.440 nonbonded pdb=" OG SER a 297 " pdb=" O TYR a 331 " model vdw 2.270 2.440 ... (remaining 82722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 131 through 352)) selection = chain 'B' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.340 Find NCS groups from input model: 0.530 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.003 0.050 10821 Z= 0.203 Angle : 0.513 5.997 14678 Z= 0.282 Chirality : 0.042 0.206 1567 Planarity : 0.003 0.033 1877 Dihedral : 12.971 84.636 3917 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1325 helix: 2.14 (0.44), residues: 146 sheet: -1.50 (0.31), residues: 289 loop : -1.30 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 150 HIS 0.003 0.001 HIS B 181 PHE 0.012 0.001 PHE a 163 TYR 0.012 0.001 TYR A 331 ARG 0.003 0.000 ARG b 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.7846 (p90) cc_final: 0.7509 (p90) REVERT: A 157 ASP cc_start: 0.7620 (m-30) cc_final: 0.7420 (m-30) REVERT: A 274 GLU cc_start: 0.8095 (tp30) cc_final: 0.7879 (mm-30) REVERT: A 276 ASP cc_start: 0.8163 (p0) cc_final: 0.7948 (p0) REVERT: A 342 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.4862 (pt0) REVERT: a 11 LYS cc_start: 0.8366 (mttt) cc_final: 0.7856 (mtmm) REVERT: a 276 ASP cc_start: 0.8419 (t0) cc_final: 0.8214 (t0) REVERT: a 292 ASP cc_start: 0.7119 (p0) cc_final: 0.6859 (t70) REVERT: a 344 ASN cc_start: 0.8189 (p0) cc_final: 0.7958 (p0) REVERT: B 70 GLN cc_start: 0.7506 (tt0) cc_final: 0.7189 (pt0) REVERT: B 134 LEU cc_start: 0.8298 (tt) cc_final: 0.8059 (tt) REVERT: B 147 ARG cc_start: 0.7098 (ptt-90) cc_final: 0.6431 (ptm160) REVERT: B 179 CYS cc_start: 0.7584 (m) cc_final: 0.7264 (m) REVERT: B 342 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7386 (tm-30) REVERT: b 272 LYS cc_start: 0.8488 (mppt) cc_final: 0.8005 (mtpt) REVERT: b 299 ARG cc_start: 0.7694 (mtm180) cc_final: 0.7456 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 230 average time/residue: 0.2245 time to fit residues: 73.7078 Evaluate side-chains 156 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 48 ASN A 349 GLN a 207 ASN a 288 GLN b 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10821 Z= 0.215 Angle : 0.489 6.047 14678 Z= 0.257 Chirality : 0.042 0.141 1567 Planarity : 0.003 0.034 1877 Dihedral : 4.452 55.149 1424 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.83 % Allowed : 6.53 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1325 helix: 2.50 (0.44), residues: 146 sheet: -1.26 (0.31), residues: 299 loop : -1.34 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 330 HIS 0.003 0.001 HIS B 254 PHE 0.011 0.001 PHE A 277 TYR 0.010 0.001 TYR B 256 ARG 0.002 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7592 (tp40) cc_final: 0.7375 (tp40) REVERT: A 124 PHE cc_start: 0.7854 (p90) cc_final: 0.7513 (p90) REVERT: A 274 GLU cc_start: 0.7992 (tp30) cc_final: 0.7769 (mm-30) REVERT: A 342 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5476 (pt0) REVERT: a 11 LYS cc_start: 0.8310 (mttt) cc_final: 0.7782 (mtmt) REVERT: B 70 GLN cc_start: 0.7277 (tt0) cc_final: 0.6867 (pt0) REVERT: B 134 LEU cc_start: 0.8384 (tt) cc_final: 0.8144 (tt) REVERT: B 147 ARG cc_start: 0.7072 (ptt-90) cc_final: 0.6349 (ptm160) REVERT: B 179 CYS cc_start: 0.7572 (m) cc_final: 0.7204 (m) REVERT: B 342 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7389 (tm-30) REVERT: b 272 LYS cc_start: 0.8538 (mppt) cc_final: 0.7913 (mtpt) REVERT: b 299 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7445 (mtm-85) outliers start: 21 outliers final: 15 residues processed: 161 average time/residue: 0.2074 time to fit residues: 48.6746 Evaluate side-chains 163 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10821 Z= 0.268 Angle : 0.500 6.378 14678 Z= 0.261 Chirality : 0.042 0.145 1567 Planarity : 0.003 0.036 1877 Dihedral : 4.483 49.495 1424 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.09 % Allowed : 9.32 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1325 helix: 2.52 (0.44), residues: 146 sheet: -1.27 (0.31), residues: 291 loop : -1.34 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 330 HIS 0.004 0.001 HIS B 254 PHE 0.010 0.002 PHE B 277 TYR 0.011 0.001 TYR B 256 ARG 0.003 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 342 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5967 (pt0) REVERT: a 11 LYS cc_start: 0.8330 (mttt) cc_final: 0.7768 (mtmt) REVERT: B 70 GLN cc_start: 0.7284 (tt0) cc_final: 0.6871 (pt0) REVERT: B 134 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8196 (tt) REVERT: B 147 ARG cc_start: 0.7034 (ptt-90) cc_final: 0.6332 (ptm160) REVERT: B 179 CYS cc_start: 0.7589 (m) cc_final: 0.7199 (m) REVERT: B 342 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7410 (tm-30) REVERT: b 272 LYS cc_start: 0.8480 (mppt) cc_final: 0.7880 (mtpt) REVERT: b 299 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7452 (mtm-85) outliers start: 24 outliers final: 16 residues processed: 163 average time/residue: 0.2120 time to fit residues: 50.4917 Evaluate side-chains 163 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 46 ILE Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10821 Z= 0.237 Angle : 0.482 6.178 14678 Z= 0.252 Chirality : 0.042 0.142 1567 Planarity : 0.003 0.037 1877 Dihedral : 4.412 44.287 1424 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.35 % Allowed : 11.32 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1325 helix: 2.60 (0.44), residues: 146 sheet: -1.31 (0.30), residues: 298 loop : -1.30 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.004 0.001 HIS B 254 PHE 0.011 0.001 PHE B 277 TYR 0.014 0.001 TYR a 256 ARG 0.002 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8348 (mttt) cc_final: 0.7769 (mtmt) REVERT: a 265 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8449 (t) REVERT: B 70 GLN cc_start: 0.7284 (tt0) cc_final: 0.6851 (pt0) REVERT: B 134 LEU cc_start: 0.8466 (tt) cc_final: 0.8212 (tt) REVERT: B 147 ARG cc_start: 0.7065 (ptt-90) cc_final: 0.6335 (ptm160) REVERT: B 342 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7414 (tm-30) REVERT: b 272 LYS cc_start: 0.8519 (mppt) cc_final: 0.7854 (mtpt) REVERT: b 299 ARG cc_start: 0.7678 (mtm180) cc_final: 0.7382 (mtm-85) outliers start: 27 outliers final: 16 residues processed: 164 average time/residue: 0.1973 time to fit residues: 47.1914 Evaluate side-chains 163 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 265 VAL Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10821 Z= 0.294 Angle : 0.515 6.362 14678 Z= 0.269 Chirality : 0.042 0.147 1567 Planarity : 0.003 0.038 1877 Dihedral : 4.170 17.164 1421 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.44 % Allowed : 12.63 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1325 helix: 2.54 (0.44), residues: 146 sheet: -1.13 (0.30), residues: 305 loop : -1.34 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 80 HIS 0.005 0.001 HIS B 254 PHE 0.010 0.002 PHE A 277 TYR 0.019 0.002 TYR a 256 ARG 0.003 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8353 (mttt) cc_final: 0.7763 (mtmt) REVERT: a 265 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8552 (t) REVERT: B 70 GLN cc_start: 0.7228 (tt0) cc_final: 0.6836 (pt0) REVERT: B 134 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 147 ARG cc_start: 0.7107 (ptt-90) cc_final: 0.6346 (ptm160) REVERT: B 179 CYS cc_start: 0.7610 (m) cc_final: 0.7201 (m) REVERT: B 342 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7391 (tm-30) REVERT: b 272 LYS cc_start: 0.8591 (mppt) cc_final: 0.7869 (mtpt) REVERT: b 340 GLU cc_start: 0.7357 (tp30) cc_final: 0.7039 (tp30) outliers start: 28 outliers final: 17 residues processed: 165 average time/residue: 0.1893 time to fit residues: 46.1611 Evaluate side-chains 162 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 46 ILE Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 265 VAL Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10821 Z= 0.311 Angle : 0.528 6.102 14678 Z= 0.276 Chirality : 0.043 0.155 1567 Planarity : 0.003 0.041 1877 Dihedral : 4.302 19.699 1421 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.70 % Allowed : 12.80 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1325 helix: 2.51 (0.44), residues: 146 sheet: -1.13 (0.31), residues: 305 loop : -1.37 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 80 HIS 0.005 0.001 HIS B 254 PHE 0.011 0.002 PHE B 323 TYR 0.021 0.002 TYR a 256 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8358 (mttt) cc_final: 0.7762 (mtmt) REVERT: a 265 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 70 GLN cc_start: 0.7199 (tt0) cc_final: 0.6809 (pt0) REVERT: B 134 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8261 (tt) REVERT: B 147 ARG cc_start: 0.7091 (ptt-90) cc_final: 0.6386 (ptm160) REVERT: B 170 LYS cc_start: 0.7783 (ptmt) cc_final: 0.7381 (ptpp) REVERT: B 342 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7410 (tm-30) REVERT: b 272 LYS cc_start: 0.8626 (mppt) cc_final: 0.7882 (mtpt) REVERT: b 340 GLU cc_start: 0.7381 (tp30) cc_final: 0.7084 (tp30) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.2002 time to fit residues: 49.6547 Evaluate side-chains 164 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 46 ILE Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 166 ASN Chi-restraints excluded: chain a residue 265 VAL Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10821 Z= 0.357 Angle : 0.561 7.555 14678 Z= 0.293 Chirality : 0.044 0.172 1567 Planarity : 0.004 0.040 1877 Dihedral : 4.448 17.714 1421 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.70 % Allowed : 13.85 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1325 helix: 2.46 (0.44), residues: 146 sheet: -1.18 (0.31), residues: 286 loop : -1.45 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.005 0.001 HIS B 254 PHE 0.012 0.002 PHE B 323 TYR 0.022 0.002 TYR a 256 ARG 0.004 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8392 (mttt) cc_final: 0.7786 (mtmt) REVERT: B 70 GLN cc_start: 0.7206 (tt0) cc_final: 0.6804 (pt0) REVERT: B 134 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8257 (tt) REVERT: B 147 ARG cc_start: 0.7421 (ptt-90) cc_final: 0.6663 (ptm160) REVERT: B 170 LYS cc_start: 0.7771 (ptmt) cc_final: 0.7358 (ptpp) REVERT: B 342 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7423 (tm-30) REVERT: b 340 GLU cc_start: 0.7383 (tp30) cc_final: 0.7093 (tp30) outliers start: 31 outliers final: 22 residues processed: 163 average time/residue: 0.1972 time to fit residues: 47.4846 Evaluate side-chains 160 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 46 ILE Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 166 ASN Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 276 ASP Chi-restraints excluded: chain b residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 38 optimal weight: 0.0670 chunk 24 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10821 Z= 0.137 Angle : 0.451 6.884 14678 Z= 0.239 Chirality : 0.040 0.132 1567 Planarity : 0.003 0.037 1877 Dihedral : 3.949 16.099 1421 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.22 % Allowed : 14.98 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1325 helix: 2.74 (0.44), residues: 146 sheet: -0.97 (0.31), residues: 285 loop : -1.27 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.003 0.001 HIS B 181 PHE 0.012 0.001 PHE A 277 TYR 0.018 0.001 TYR a 256 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8331 (mttt) cc_final: 0.7774 (mtmt) REVERT: a 48 ASN cc_start: 0.7382 (m110) cc_final: 0.6946 (m-40) REVERT: a 345 MET cc_start: 0.7416 (mtp) cc_final: 0.7102 (mtp) REVERT: B 70 GLN cc_start: 0.7185 (tt0) cc_final: 0.6787 (pt0) REVERT: B 147 ARG cc_start: 0.7301 (ptt-90) cc_final: 0.6517 (ptm160) REVERT: B 342 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7267 (tm-30) REVERT: b 272 LYS cc_start: 0.8623 (mppt) cc_final: 0.7858 (mtpt) REVERT: b 299 ARG cc_start: 0.7662 (mtm180) cc_final: 0.7274 (mtm-85) REVERT: b 340 GLU cc_start: 0.7392 (tp30) cc_final: 0.7075 (tp30) outliers start: 14 outliers final: 12 residues processed: 154 average time/residue: 0.2064 time to fit residues: 46.6081 Evaluate side-chains 157 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 166 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 117 optimal weight: 0.0050 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 0.0070 chunk 124 optimal weight: 9.9990 overall best weight: 2.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10821 Z= 0.296 Angle : 0.522 6.348 14678 Z= 0.272 Chirality : 0.043 0.147 1567 Planarity : 0.003 0.038 1877 Dihedral : 4.173 17.122 1421 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.48 % Allowed : 15.07 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.22), residues: 1325 helix: 2.68 (0.44), residues: 146 sheet: -1.15 (0.31), residues: 288 loop : -1.33 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.004 0.001 HIS B 254 PHE 0.010 0.002 PHE B 323 TYR 0.019 0.001 TYR a 256 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8355 (mttt) cc_final: 0.7793 (mtmt) REVERT: a 48 ASN cc_start: 0.7447 (m110) cc_final: 0.7009 (m-40) REVERT: B 70 GLN cc_start: 0.7213 (tt0) cc_final: 0.6812 (pt0) REVERT: B 147 ARG cc_start: 0.7474 (ptt-90) cc_final: 0.6694 (ptm160) REVERT: B 342 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7425 (tm-30) REVERT: b 340 GLU cc_start: 0.7452 (tp30) cc_final: 0.7108 (tp30) outliers start: 17 outliers final: 16 residues processed: 153 average time/residue: 0.1980 time to fit residues: 45.2046 Evaluate side-chains 159 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 166 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 276 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.0470 chunk 59 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10821 Z= 0.119 Angle : 0.442 7.845 14678 Z= 0.232 Chirality : 0.040 0.134 1567 Planarity : 0.003 0.038 1877 Dihedral : 3.799 15.028 1421 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.05 % Allowed : 15.77 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1325 helix: 2.89 (0.45), residues: 146 sheet: -1.05 (0.31), residues: 292 loop : -1.18 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 80 HIS 0.003 0.000 HIS B 181 PHE 0.012 0.001 PHE A 277 TYR 0.018 0.001 TYR a 256 ARG 0.001 0.000 ARG A 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7919 (tptt) cc_final: 0.7667 (tptt) REVERT: A 30 GLU cc_start: 0.7100 (mp0) cc_final: 0.6858 (mp0) REVERT: a 11 LYS cc_start: 0.8320 (mttt) cc_final: 0.7736 (mtmt) REVERT: a 48 ASN cc_start: 0.7357 (m110) cc_final: 0.6920 (m-40) REVERT: B 70 GLN cc_start: 0.7160 (tt0) cc_final: 0.6759 (pt0) REVERT: B 147 ARG cc_start: 0.7279 (ptt-90) cc_final: 0.6483 (ptm160) REVERT: B 333 MET cc_start: 0.8279 (ttt) cc_final: 0.7985 (ttt) REVERT: B 342 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7291 (tm-30) REVERT: b 272 LYS cc_start: 0.8606 (mppt) cc_final: 0.7827 (mtpt) REVERT: b 299 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7224 (mtm-85) REVERT: b 340 GLU cc_start: 0.7354 (tp30) cc_final: 0.7097 (tp30) outliers start: 12 outliers final: 10 residues processed: 164 average time/residue: 0.2058 time to fit residues: 49.8531 Evaluate side-chains 163 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.155864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097113 restraints weight = 10997.464| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.51 r_work: 0.2891 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10821 Z= 0.238 Angle : 0.491 6.696 14678 Z= 0.256 Chirality : 0.042 0.141 1567 Planarity : 0.003 0.037 1877 Dihedral : 3.956 16.104 1421 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.13 % Allowed : 16.03 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1325 helix: 2.85 (0.44), residues: 146 sheet: -1.07 (0.31), residues: 288 loop : -1.23 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 80 HIS 0.004 0.001 HIS B 254 PHE 0.010 0.001 PHE a 163 TYR 0.019 0.001 TYR a 256 ARG 0.003 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.18 seconds wall clock time: 46 minutes 45.60 seconds (2805.60 seconds total)