Starting phenix.real_space_refine on Sat Mar 16 06:49:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/03_2024/6n25_9323_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/03_2024/6n25_9323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/03_2024/6n25_9323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/03_2024/6n25_9323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/03_2024/6n25_9323_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/03_2024/6n25_9323_neut.pdb" } resolution = 2.7 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= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 65 5.16 5 C 9145 2.51 5 N 2275 2.21 5 O 2450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13940 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2787 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2787 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2787 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2787 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2787 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.73, per 1000 atoms: 0.48 Number of scatterers: 13940 At special positions: 0 Unit cell: (96.832, 96.832, 112.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 65 16.00 O 2450 8.00 N 2275 7.00 C 9145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.05 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: 4.82 Conformation dependent library (CDL) restraints added in 2.2 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.927A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 23' Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.746A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.613A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.544A pdb=" N LYS A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.846A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.522A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.503A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.927A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 23' Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.611A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.544A pdb=" N LYS B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.845A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.523A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.503A pdb=" N ASP B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.926A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 23' Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 76 Processing helix chain 'C' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.612A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 removed outlier: 3.543A pdb=" N LYS C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.846A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.523A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.504A pdb=" N ASP C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.927A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 23' Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.539A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.664A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.613A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.795A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.543A pdb=" N LYS D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.845A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.523A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.590A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.503A pdb=" N ASP D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.926A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 23' Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.538A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 53 removed outlier: 3.665A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.813A pdb=" N LEU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 98 removed outlier: 3.623A pdb=" N SER E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.747A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.612A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.794A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.544A pdb=" N LYS E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.846A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.522A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.591A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE E 247 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.504A pdb=" N ASP E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2370 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: 4.19 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4325 1.34 - 1.46: 3840 1.46 - 1.59: 6055 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 14320 Sorted by residual: bond pdb=" CB MET A 107 " pdb=" CG MET A 107 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" CB MET E 107 " pdb=" CG MET E 107 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CB MET B 107 " pdb=" CG MET B 107 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB MET C 107 " pdb=" CG MET C 107 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 ... (remaining 14315 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.75: 378 106.75 - 113.57: 7671 113.57 - 120.39: 6060 120.39 - 127.22: 5184 127.22 - 134.04: 182 Bond angle restraints: 19475 Sorted by residual: angle pdb=" CA ARG C 13 " pdb=" CB ARG C 13 " pdb=" CG ARG C 13 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG A 13 " pdb=" CB ARG A 13 " pdb=" CG ARG A 13 " ideal model delta sigma weight residual 114.10 121.92 -7.82 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA ARG B 13 " pdb=" CB ARG B 13 " pdb=" CG ARG B 13 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA ARG E 13 " pdb=" CB ARG E 13 " pdb=" CG ARG E 13 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA ARG D 13 " pdb=" CB ARG D 13 " pdb=" CG ARG D 13 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 ... (remaining 19470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 7977 15.13 - 30.25: 323 30.25 - 45.38: 90 45.38 - 60.51: 0 60.51 - 75.63: 5 Dihedral angle restraints: 8395 sinusoidal: 3375 harmonic: 5020 Sorted by residual: dihedral pdb=" CA SER B 231 " pdb=" C SER B 231 " pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA SER A 231 " pdb=" C SER A 231 " pdb=" N ILE A 232 " pdb=" CA ILE A 232 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA SER C 231 " pdb=" C SER C 231 " pdb=" N ILE C 232 " pdb=" CA ILE C 232 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1227 0.044 - 0.087: 722 0.087 - 0.130: 161 0.130 - 0.174: 20 0.174 - 0.217: 20 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CA ARG A 13 " pdb=" N ARG A 13 " pdb=" C ARG A 13 " pdb=" CB ARG A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 54 " pdb=" CB LEU A 54 " pdb=" CD1 LEU A 54 " pdb=" CD2 LEU A 54 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU D 54 " pdb=" CB LEU D 54 " pdb=" CD1 LEU D 54 " pdb=" CD2 LEU D 54 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2147 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 229 " 0.014 2.00e-02 2.50e+03 1.28e-02 4.09e+00 pdb=" CG TRP E 229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 229 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 229 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 229 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 229 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 229 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 229 " 0.014 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP C 229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 229 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 229 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 229 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 229 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " 0.014 2.00e-02 2.50e+03 1.27e-02 4.03e+00 pdb=" CG TRP A 229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.000 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4485 2.83 - 3.34: 12069 3.34 - 3.86: 23129 3.86 - 4.38: 28244 4.38 - 4.90: 47179 Nonbonded interactions: 115106 Sorted by model distance: nonbonded pdb=" NH2 ARG A 218 " pdb=" OD2 ASP E 104 " model vdw 2.307 2.520 nonbonded pdb=" OD2 ASP A 104 " pdb=" NH2 ARG B 218 " model vdw 2.308 2.520 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.315 2.520 nonbonded pdb=" OE1 GLU C 63 " pdb=" OH TYR C 264 " model vdw 2.316 2.440 nonbonded pdb=" OE1 GLU B 63 " pdb=" OH TYR B 264 " model vdw 2.316 2.440 ... (remaining 115101 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.120 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: 1.500 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 35.820 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.008 0.064 14320 Z= 0.489 Angle : 0.850 8.494 19475 Z= 0.444 Chirality : 0.054 0.217 2150 Planarity : 0.006 0.045 2435 Dihedral : 9.284 75.632 5140 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.12 (0.11), residues: 1680 helix: -4.37 (0.05), residues: 1155 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP E 229 HIS 0.011 0.003 HIS D 326 PHE 0.017 0.003 PHE D 36 TYR 0.017 0.003 TYR E 97 ARG 0.007 0.001 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.692 Fit side-chains REVERT: A 60 LEU cc_start: 0.9094 (tt) cc_final: 0.8835 (tm) REVERT: B 149 LYS cc_start: 0.8822 (mttt) cc_final: 0.8575 (mtpt) REVERT: D 58 GLN cc_start: 0.8821 (mt0) cc_final: 0.8292 (mt0) REVERT: E 21 LEU cc_start: 0.8470 (pp) cc_final: 0.8263 (pt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 1.4611 time to fit residues: 450.9435 Evaluate side-chains 108 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN C 23 GLN C 316 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14320 Z= 0.185 Angle : 0.561 6.318 19475 Z= 0.302 Chirality : 0.040 0.162 2150 Planarity : 0.005 0.032 2435 Dihedral : 4.314 15.782 1880 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.09 % Allowed : 8.69 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 1680 helix: -1.17 (0.13), residues: 1190 sheet: None (None), residues: 0 loop : -2.20 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 229 HIS 0.003 0.001 HIS E 326 PHE 0.019 0.002 PHE B 272 TYR 0.017 0.001 TYR A 236 ARG 0.003 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.647 Fit side-chains REVERT: A 262 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8981 (mttm) REVERT: C 21 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8108 (pt) REVERT: D 7 ASN cc_start: 0.8601 (t0) cc_final: 0.8333 (t0) REVERT: D 163 MET cc_start: 0.9009 (ttm) cc_final: 0.8687 (ttp) REVERT: E 56 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7771 (tp30) outliers start: 32 outliers final: 9 residues processed: 157 average time/residue: 1.0836 time to fit residues: 190.5272 Evaluate side-chains 105 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 169 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14320 Z= 0.287 Angle : 0.546 6.727 19475 Z= 0.285 Chirality : 0.041 0.159 2150 Planarity : 0.004 0.034 2435 Dihedral : 4.011 13.597 1880 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.27 % Allowed : 10.46 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1680 helix: 0.07 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 182 HIS 0.004 0.001 HIS A 326 PHE 0.020 0.002 PHE B 272 TYR 0.014 0.001 TYR D 97 ARG 0.002 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 97 time to evaluate : 2.192 Fit side-chains REVERT: C 107 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8276 (ptm) REVERT: C 169 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: D 203 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7252 (t0) REVERT: D 306 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7635 (mt-10) outliers start: 50 outliers final: 16 residues processed: 132 average time/residue: 0.9580 time to fit residues: 144.1640 Evaluate side-chains 115 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 0.4980 chunk 159 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN E 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14320 Z= 0.125 Angle : 0.435 5.715 19475 Z= 0.232 Chirality : 0.037 0.159 2150 Planarity : 0.003 0.031 2435 Dihedral : 3.763 12.494 1880 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.42 % Allowed : 10.92 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1680 helix: 0.88 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 229 HIS 0.001 0.000 HIS D 267 PHE 0.015 0.001 PHE B 272 TYR 0.011 0.001 TYR C 236 ARG 0.002 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.698 Fit side-chains REVERT: A 21 LEU cc_start: 0.8375 (pp) cc_final: 0.8126 (pt) REVERT: B 21 LEU cc_start: 0.8191 (pp) cc_final: 0.7843 (pt) REVERT: C 21 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7939 (pt) REVERT: D 236 TYR cc_start: 0.8052 (m-10) cc_final: 0.7836 (m-10) outliers start: 37 outliers final: 13 residues processed: 127 average time/residue: 0.8846 time to fit residues: 128.7302 Evaluate side-chains 116 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14320 Z= 0.308 Angle : 0.522 5.374 19475 Z= 0.277 Chirality : 0.042 0.157 2150 Planarity : 0.004 0.036 2435 Dihedral : 3.795 13.772 1880 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.88 % Allowed : 10.98 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1680 helix: 1.01 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 182 HIS 0.004 0.001 HIS A 326 PHE 0.019 0.002 PHE C 272 TYR 0.014 0.001 TYR A 236 ARG 0.002 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 1.600 Fit side-chains REVERT: A 7 ASN cc_start: 0.8657 (t0) cc_final: 0.8365 (t160) REVERT: C 21 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8151 (pt) outliers start: 44 outliers final: 27 residues processed: 125 average time/residue: 0.8441 time to fit residues: 121.3096 Evaluate side-chains 126 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.8520 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14320 Z= 0.261 Angle : 0.496 5.702 19475 Z= 0.263 Chirality : 0.041 0.159 2150 Planarity : 0.003 0.034 2435 Dihedral : 3.782 13.582 1880 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.14 % Allowed : 10.98 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1680 helix: 1.16 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.61 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.003 0.001 HIS A 326 PHE 0.022 0.002 PHE C 272 TYR 0.013 0.001 TYR C 236 ARG 0.002 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 98 time to evaluate : 1.755 Fit side-chains REVERT: A 7 ASN cc_start: 0.8650 (t0) cc_final: 0.8361 (t160) REVERT: C 21 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8091 (pt) outliers start: 48 outliers final: 28 residues processed: 125 average time/residue: 0.8636 time to fit residues: 123.7579 Evaluate side-chains 128 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14320 Z= 0.183 Angle : 0.462 6.279 19475 Z= 0.248 Chirality : 0.039 0.156 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.690 13.116 1880 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.75 % Allowed : 11.50 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1680 helix: 1.29 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 182 HIS 0.002 0.000 HIS A 326 PHE 0.019 0.001 PHE C 272 TYR 0.016 0.001 TYR C 236 ARG 0.002 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 1.364 Fit side-chains REVERT: A 7 ASN cc_start: 0.8632 (t0) cc_final: 0.8407 (t0) REVERT: A 19 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: C 21 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7975 (pt) REVERT: D 21 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8227 (pt) outliers start: 42 outliers final: 30 residues processed: 129 average time/residue: 0.8413 time to fit residues: 124.8768 Evaluate side-chains 137 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8485 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14320 Z= 0.176 Angle : 0.464 6.787 19475 Z= 0.248 Chirality : 0.039 0.157 2150 Planarity : 0.003 0.036 2435 Dihedral : 3.628 12.896 1880 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.55 % Allowed : 11.50 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1680 helix: 1.38 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 182 HIS 0.005 0.001 HIS C 326 PHE 0.022 0.001 PHE C 272 TYR 0.013 0.001 TYR A 236 ARG 0.001 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 1.599 Fit side-chains REVERT: A 7 ASN cc_start: 0.8626 (t0) cc_final: 0.8405 (t0) REVERT: B 21 LEU cc_start: 0.8310 (pp) cc_final: 0.7959 (pt) REVERT: D 21 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8166 (pt) outliers start: 39 outliers final: 29 residues processed: 122 average time/residue: 0.8073 time to fit residues: 114.0274 Evaluate side-chains 129 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14320 Z= 0.179 Angle : 0.460 6.356 19475 Z= 0.246 Chirality : 0.039 0.156 2150 Planarity : 0.003 0.036 2435 Dihedral : 3.604 14.559 1880 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.48 % Allowed : 11.70 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1680 helix: 1.44 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.46 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 182 HIS 0.003 0.000 HIS C 326 PHE 0.020 0.001 PHE C 272 TYR 0.012 0.001 TYR A 236 ARG 0.002 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 100 time to evaluate : 1.714 Fit side-chains REVERT: A 7 ASN cc_start: 0.8613 (t0) cc_final: 0.8392 (t0) REVERT: A 19 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: A 60 LEU cc_start: 0.8341 (mt) cc_final: 0.8133 (mm) REVERT: D 21 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8165 (pt) outliers start: 38 outliers final: 32 residues processed: 122 average time/residue: 0.8130 time to fit residues: 115.2142 Evaluate side-chains 133 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14320 Z= 0.214 Angle : 0.478 5.969 19475 Z= 0.254 Chirality : 0.040 0.157 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.631 13.446 1880 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.35 % Allowed : 11.83 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1680 helix: 1.40 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 182 HIS 0.003 0.001 HIS C 326 PHE 0.024 0.002 PHE C 272 TYR 0.014 0.001 TYR A 236 ARG 0.001 0.000 ARG E 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.542 Fit side-chains REVERT: A 7 ASN cc_start: 0.8639 (t0) cc_final: 0.8414 (t0) REVERT: A 19 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: A 60 LEU cc_start: 0.8394 (mt) cc_final: 0.8190 (mm) REVERT: D 21 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8212 (pt) outliers start: 36 outliers final: 31 residues processed: 121 average time/residue: 0.8340 time to fit residues: 116.7282 Evaluate side-chains 131 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.098416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.077273 restraints weight = 18609.120| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.46 r_work: 0.2769 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14320 Z= 0.153 Angle : 0.447 5.846 19475 Z= 0.240 Chirality : 0.038 0.156 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.571 13.395 1880 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.83 % Allowed : 12.48 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1680 helix: 1.54 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.42 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 182 HIS 0.002 0.000 HIS C 326 PHE 0.026 0.001 PHE C 272 TYR 0.012 0.001 TYR C 236 ARG 0.002 0.000 ARG A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3456.60 seconds wall clock time: 62 minutes 28.01 seconds (3748.01 seconds total)