Starting phenix.real_space_refine on Sun Aug 4 13:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/08_2024/8wbc_37420_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/08_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_37420/08_2024/8wbc_37420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/08_2024/8wbc_37420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/08_2024/8wbc_37420_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbc_37420/08_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-5409/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: 6.06, 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: 3.61 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: 1.20 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: 2.91 Time building geometry restraints manager: 4.03 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 3.040 nonbonded pdb=" OG SER B 297 " pdb=" O TYR B 331 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 283 " pdb=" OH TYR B 331 " model vdw 2.244 3.040 nonbonded pdb=" O TRP a 68 " pdb=" OG1 THR a 72 " model vdw 2.260 3.040 nonbonded pdb=" OG SER a 297 " pdb=" O TYR a 331 " model vdw 2.270 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.900 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.630 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- 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 : 1.217 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: 0.2095 time to fit residues: 68.5532 Evaluate side-chains 156 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 118 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 166 ASN b 26 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10821 Z= 0.170 Angle : 0.482 5.749 14678 Z= 0.255 Chirality : 0.042 0.136 1567 Planarity : 0.003 0.034 1877 Dihedral : 4.411 54.187 1424 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.74 % Allowed : 5.66 % Favored : 92.60 % 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: 2.54 (0.44), residues: 146 sheet: -1.36 (0.31), residues: 292 loop : -1.27 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 330 HIS 0.003 0.001 HIS B 181 PHE 0.011 0.001 PHE B 277 TYR 0.010 0.001 TYR a 158 ARG 0.002 0.000 ARG b 294 *********************** 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 177 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7586 (tp40) cc_final: 0.7386 (tp40) REVERT: A 274 GLU cc_start: 0.8007 (tp30) cc_final: 0.7785 (mm-30) REVERT: A 342 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5366 (pt0) REVERT: a 11 LYS cc_start: 0.8298 (mttt) cc_final: 0.7776 (mtmt) REVERT: a 302 THR cc_start: 0.8471 (t) cc_final: 0.8256 (p) REVERT: B 70 GLN cc_start: 0.7292 (tt0) cc_final: 0.6901 (pt0) REVERT: B 134 LEU cc_start: 0.8332 (tt) cc_final: 0.8069 (tt) REVERT: B 147 ARG cc_start: 0.7279 (ptt-90) cc_final: 0.6476 (ptm160) REVERT: B 179 CYS cc_start: 0.7570 (m) cc_final: 0.7220 (m) REVERT: B 342 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7402 (tm-30) REVERT: b 272 LYS cc_start: 0.8518 (mppt) cc_final: 0.7913 (mtpt) REVERT: b 299 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7352 (mtm-85) outliers start: 20 outliers final: 10 residues processed: 165 average time/residue: 0.2090 time to fit residues: 50.2698 Evaluate side-chains 159 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 342 GLU 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 350 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain b residue 67 MET 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: 5.9990 chunk 36 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 a 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10821 Z= 0.479 Angle : 0.621 6.992 14678 Z= 0.325 Chirality : 0.047 0.164 1567 Planarity : 0.004 0.034 1877 Dihedral : 4.896 51.808 1424 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.35 % Allowed : 9.76 % Favored : 87.89 % 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: -1.49 (0.22), residues: 1325 helix: 2.27 (0.43), residues: 146 sheet: -1.49 (0.31), residues: 284 loop : -1.45 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 330 HIS 0.006 0.001 HIS B 254 PHE 0.015 0.002 PHE a 163 TYR 0.021 0.002 TYR a 158 ARG 0.006 0.001 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 177 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8354 (mttt) cc_final: 0.7724 (mtmt) REVERT: B 70 GLN cc_start: 0.7357 (tt0) cc_final: 0.6890 (pt0) REVERT: B 134 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8155 (tt) REVERT: B 147 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.6717 (ptm160) REVERT: B 170 LYS cc_start: 0.7698 (ptmt) cc_final: 0.7329 (ptpp) REVERT: B 179 CYS cc_start: 0.7652 (m) cc_final: 0.7282 (m) REVERT: B 342 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7416 (tm-30) REVERT: b 272 LYS cc_start: 0.8504 (mppt) cc_final: 0.7855 (mtpt) outliers start: 27 outliers final: 17 residues processed: 164 average time/residue: 0.2033 time to fit residues: 49.1141 Evaluate side-chains 161 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 264 THR Chi-restraints excluded: chain A residue 307 LEU 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 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 THR 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 Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1519 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= 0.297 Angle : 0.532 6.384 14678 Z= 0.280 Chirality : 0.043 0.151 1567 Planarity : 0.003 0.035 1877 Dihedral : 4.360 17.484 1421 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.26 % Allowed : 11.85 % Favored : 85.89 % 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: -1.43 (0.22), residues: 1325 helix: 2.35 (0.43), residues: 147 sheet: -1.47 (0.31), residues: 277 loop : -1.42 (0.18), residues: 901 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 0.012 0.002 PHE B 277 TYR 0.017 0.002 TYR a 158 ARG 0.002 0.000 ARG A 182 *********************** 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 184 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7129 (mp0) cc_final: 0.6907 (mp0) REVERT: a 11 LYS cc_start: 0.8366 (mttt) cc_final: 0.7756 (mtmt) REVERT: a 203 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8421 (mt-10) REVERT: a 265 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8468 (t) REVERT: a 302 THR cc_start: 0.8398 (t) cc_final: 0.8102 (p) REVERT: B 70 GLN cc_start: 0.7320 (tt0) cc_final: 0.6880 (pt0) REVERT: B 134 LEU cc_start: 0.8476 (tt) cc_final: 0.8167 (tt) REVERT: B 147 ARG cc_start: 0.7480 (ptt-90) cc_final: 0.6678 (ptm160) REVERT: B 179 CYS cc_start: 0.7609 (m) cc_final: 0.7208 (m) REVERT: B 342 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7238 (tm-30) REVERT: b 272 LYS cc_start: 0.8586 (mppt) cc_final: 0.7887 (mtpt) outliers start: 26 outliers final: 14 residues processed: 171 average time/residue: 0.1882 time to fit residues: 47.8608 Evaluate side-chains 165 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10821 Z= 0.392 Angle : 0.581 7.250 14678 Z= 0.304 Chirality : 0.045 0.169 1567 Planarity : 0.004 0.040 1877 Dihedral : 4.537 18.991 1421 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.70 % Allowed : 12.72 % Favored : 84.58 % 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: -1.51 (0.21), residues: 1325 helix: 2.29 (0.43), residues: 146 sheet: -1.47 (0.30), residues: 287 loop : -1.48 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 80 HIS 0.006 0.001 HIS B 254 PHE 0.011 0.002 PHE B 323 TYR 0.024 0.002 TYR a 158 ARG 0.004 0.000 ARG A 182 *********************** 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 183 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7179 (mp0) cc_final: 0.6792 (mp0) REVERT: A 37 GLU cc_start: 0.7414 (pm20) cc_final: 0.7210 (mt-10) REVERT: a 11 LYS cc_start: 0.8375 (mttt) cc_final: 0.7759 (mtmt) REVERT: a 203 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8416 (mt-10) REVERT: a 302 THR cc_start: 0.8407 (t) cc_final: 0.8103 (p) REVERT: B 70 GLN cc_start: 0.7220 (tt0) cc_final: 0.6825 (pt0) REVERT: B 134 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8101 (tt) REVERT: B 147 ARG cc_start: 0.7551 (ptt-90) cc_final: 0.6719 (ptm160) REVERT: B 170 LYS cc_start: 0.7755 (ptmt) cc_final: 0.7356 (ptpp) REVERT: B 342 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7245 (tm-30) REVERT: b 272 LYS cc_start: 0.8637 (mppt) cc_final: 0.7897 (mtpt) outliers start: 31 outliers final: 17 residues processed: 172 average time/residue: 0.1939 time to fit residues: 49.0601 Evaluate side-chains 159 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 264 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS 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 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.0270 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10821 Z= 0.187 Angle : 0.491 6.238 14678 Z= 0.260 Chirality : 0.041 0.136 1567 Planarity : 0.003 0.036 1877 Dihedral : 4.254 18.016 1421 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.92 % Allowed : 13.68 % Favored : 84.41 % 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: -1.30 (0.22), residues: 1325 helix: 2.46 (0.44), residues: 146 sheet: -1.28 (0.30), residues: 286 loop : -1.35 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.004 0.001 HIS B 181 PHE 0.012 0.001 PHE A 277 TYR 0.015 0.001 TYR a 158 ARG 0.002 0.000 ARG B 314 *********************** 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 176 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8355 (mttt) cc_final: 0.7768 (mtmt) REVERT: a 203 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8314 (mt-10) REVERT: a 302 THR cc_start: 0.8358 (t) cc_final: 0.8039 (p) REVERT: B 70 GLN cc_start: 0.7202 (tt0) cc_final: 0.6803 (pt0) REVERT: B 134 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8066 (tt) REVERT: B 147 ARG cc_start: 0.7420 (ptt-90) cc_final: 0.6537 (ptm160) REVERT: B 342 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7248 (tm-30) REVERT: b 272 LYS cc_start: 0.8621 (mppt) cc_final: 0.7873 (mtpt) outliers start: 22 outliers final: 16 residues processed: 170 average time/residue: 0.1964 time to fit residues: 49.2955 Evaluate side-chains 161 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 292 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 2 THR 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 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 7.9990 chunk 14 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 293 HIS B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10821 Z= 0.485 Angle : 0.632 8.369 14678 Z= 0.330 Chirality : 0.046 0.200 1567 Planarity : 0.004 0.041 1877 Dihedral : 4.682 19.581 1421 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.18 % Allowed : 15.42 % Favored : 82.40 % 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: -1.55 (0.21), residues: 1325 helix: 2.22 (0.43), residues: 145 sheet: -1.35 (0.30), residues: 296 loop : -1.56 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 80 HIS 0.007 0.002 HIS B 254 PHE 0.014 0.002 PHE B 323 TYR 0.026 0.002 TYR a 158 ARG 0.006 0.001 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: 25 poor density : 147 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: a 11 LYS cc_start: 0.8404 (mttt) cc_final: 0.7786 (mtmt) REVERT: B 70 GLN cc_start: 0.7238 (tt0) cc_final: 0.6842 (pt0) REVERT: B 134 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8044 (tt) REVERT: B 147 ARG cc_start: 0.7563 (ptt-90) cc_final: 0.6697 (ptm160) REVERT: B 192 LYS cc_start: 0.8020 (tttp) cc_final: 0.7808 (mtpp) REVERT: B 342 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7450 (tm-30) outliers start: 25 outliers final: 17 residues processed: 164 average time/residue: 0.2089 time to fit residues: 49.3125 Evaluate side-chains 160 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 346 VAL Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain b residue 29 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10821 Z= 0.173 Angle : 0.490 6.762 14678 Z= 0.260 Chirality : 0.041 0.134 1567 Planarity : 0.003 0.041 1877 Dihedral : 4.250 16.598 1421 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.00 % Allowed : 15.68 % Favored : 82.32 % 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: -1.31 (0.22), residues: 1325 helix: 2.50 (0.44), residues: 146 sheet: -1.25 (0.30), residues: 284 loop : -1.39 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 80 HIS 0.004 0.001 HIS B 181 PHE 0.013 0.001 PHE A 277 TYR 0.016 0.001 TYR a 256 ARG 0.002 0.000 ARG a 58 *********************** 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 171 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7101 (mp0) cc_final: 0.6841 (mp0) REVERT: A 331 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8819 (m-80) REVERT: a 11 LYS cc_start: 0.8346 (mttt) cc_final: 0.7781 (mtmt) REVERT: B 70 GLN cc_start: 0.7194 (tt0) cc_final: 0.6802 (pt0) REVERT: B 134 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8072 (tt) REVERT: B 147 ARG cc_start: 0.7372 (ptt-90) cc_final: 0.6490 (ptm160) REVERT: B 192 LYS cc_start: 0.8031 (tttp) cc_final: 0.7788 (mtpp) REVERT: B 342 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7247 (tm-30) REVERT: b 299 ARG cc_start: 0.7744 (mtm180) cc_final: 0.7409 (mtm-85) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.2093 time to fit residues: 49.7652 Evaluate side-chains 162 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 143 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR 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 94 LYS Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 8.9990 chunk 110 optimal weight: 0.0370 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10821 Z= 0.412 Angle : 0.594 7.306 14678 Z= 0.312 Chirality : 0.045 0.180 1567 Planarity : 0.004 0.039 1877 Dihedral : 4.552 19.073 1421 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.18 % Allowed : 16.11 % Favored : 81.71 % 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: -1.47 (0.22), residues: 1325 helix: 2.36 (0.43), residues: 145 sheet: -1.30 (0.30), residues: 296 loop : -1.52 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 80 HIS 0.006 0.001 HIS B 254 PHE 0.011 0.002 PHE B 323 TYR 0.022 0.002 TYR a 158 ARG 0.006 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 173 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7073 (mp0) cc_final: 0.6766 (mp0) REVERT: A 331 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: a 11 LYS cc_start: 0.8397 (mttt) cc_final: 0.7801 (mtmt) REVERT: B 70 GLN cc_start: 0.7218 (tt0) cc_final: 0.6821 (pt0) REVERT: B 134 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 147 ARG cc_start: 0.7618 (ptt-90) cc_final: 0.6778 (ptm160) REVERT: B 192 LYS cc_start: 0.8024 (tttp) cc_final: 0.7819 (mtpp) REVERT: B 342 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7264 (tm-30) REVERT: b 157 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: b 299 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7554 (ttm170) outliers start: 25 outliers final: 19 residues processed: 166 average time/residue: 0.2167 time to fit residues: 51.4500 Evaluate side-chains 164 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 143 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR 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 a residue 350 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 120 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10821 Z= 0.201 Angle : 0.500 7.156 14678 Z= 0.264 Chirality : 0.042 0.136 1567 Planarity : 0.003 0.039 1877 Dihedral : 4.271 16.456 1421 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.66 % Allowed : 16.81 % Favored : 81.53 % 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: -1.31 (0.22), residues: 1325 helix: 2.57 (0.44), residues: 145 sheet: -1.27 (0.30), residues: 285 loop : -1.40 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 80 HIS 0.004 0.001 HIS B 181 PHE 0.012 0.001 PHE A 277 TYR 0.018 0.001 TYR a 158 ARG 0.002 0.000 ARG A 182 ********************** 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 166 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7083 (mp0) cc_final: 0.6798 (mp0) REVERT: A 331 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: a 11 LYS cc_start: 0.8370 (mttt) cc_final: 0.7802 (mtmt) REVERT: B 70 GLN cc_start: 0.7193 (tt0) cc_final: 0.6791 (pt0) REVERT: B 134 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8071 (tt) REVERT: B 147 ARG cc_start: 0.7380 (ptt-90) cc_final: 0.6556 (ptm160) REVERT: B 192 LYS cc_start: 0.8025 (tttp) cc_final: 0.7790 (mtpp) REVERT: B 342 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7247 (tm-30) REVERT: b 157 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: b 299 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7564 (ttm170) outliers start: 19 outliers final: 16 residues processed: 160 average time/residue: 0.2066 time to fit residues: 47.8245 Evaluate side-chains 164 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 143 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR 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 a residue 350 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 157 ASP Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104830 restraints weight = 10888.660| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.65 r_work: 0.2936 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10821 Z= 0.155 Angle : 0.470 7.009 14678 Z= 0.248 Chirality : 0.041 0.142 1567 Planarity : 0.003 0.037 1877 Dihedral : 3.976 14.842 1421 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.83 % Allowed : 16.64 % Favored : 81.53 % 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: -1.16 (0.22), residues: 1325 helix: 2.72 (0.44), residues: 146 sheet: -1.26 (0.31), residues: 281 loop : -1.26 (0.18), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 80 HIS 0.004 0.001 HIS B 181 PHE 0.011 0.001 PHE A 277 TYR 0.016 0.001 TYR a 158 ARG 0.002 0.000 ARG b 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.62 seconds wall clock time: 45 minutes 32.84 seconds (2732.84 seconds total)