Starting phenix.real_space_refine on Thu Nov 16 02:31:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/11_2023/6n25_9323_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/11_2023/6n25_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_9323/11_2023/6n25_9323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/11_2023/6n25_9323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/11_2023/6n25_9323_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n25_9323/11_2023/6n25_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-1.21rc1-5144/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: 7.89, per 1000 atoms: 0.57 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: 5.93 Conformation dependent library (CDL) restraints added in 2.6 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: 1.10 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: 3.68 Time building geometry restraints manager: 5.98 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: 0.160 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: 0.020 Extract box with map and model: 1.680 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 38.620 Find NCS groups from input model: 0.970 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: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.780 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 1.4704 time to fit residues: 453.6432 Evaluate side-chains 106 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9705 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14320 Z= 0.179 Angle : 0.555 7.120 19475 Z= 0.297 Chirality : 0.039 0.159 2150 Planarity : 0.005 0.030 2435 Dihedral : 4.303 15.013 1880 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.09 % Allowed : 8.89 % Favored : 89.02 % 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: -2.33 (0.17), residues: 1680 helix: -1.15 (0.13), residues: 1190 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 490 *********************** 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 : 1.659 Fit side-chains outliers start: 32 outliers final: 6 residues processed: 156 average time/residue: 1.0812 time to fit residues: 187.5152 Evaluate side-chains 104 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.0428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2714 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= 0.188 Angle : 0.491 6.156 19475 Z= 0.259 Chirality : 0.039 0.160 2150 Planarity : 0.003 0.034 2435 Dihedral : 3.896 11.766 1880 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.75 % Allowed : 10.59 % 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: -0.61 (0.20), residues: 1680 helix: 0.26 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.91 (0.25), residues: 495 *********************** 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 143 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 101 time to evaluate : 1.241 Fit side-chains outliers start: 42 outliers final: 17 residues processed: 127 average time/residue: 0.8903 time to fit residues: 128.8080 Evaluate side-chains 112 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 8 average time/residue: 0.1575 time to fit residues: 4.3260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN C 316 GLN E 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14320 Z= 0.156 Angle : 0.448 5.069 19475 Z= 0.237 Chirality : 0.038 0.157 2150 Planarity : 0.003 0.034 2435 Dihedral : 3.751 12.357 1880 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.48 % Allowed : 10.85 % 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: 0.12 (0.20), residues: 1680 helix: 0.84 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 480 *********************** 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 142 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 1.713 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 125 average time/residue: 0.8441 time to fit residues: 120.5709 Evaluate side-chains 117 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.2418 time to fit residues: 4.8942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- 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: 0.8539 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14320 Z= 0.365 Angle : 0.557 6.186 19475 Z= 0.291 Chirality : 0.044 0.158 2150 Planarity : 0.004 0.035 2435 Dihedral : 3.850 13.945 1880 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.75 % Allowed : 11.05 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1680 helix: 0.92 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.77 (0.25), residues: 490 *********************** 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 140 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 1.724 Fit side-chains outliers start: 42 outliers final: 20 residues processed: 126 average time/residue: 0.9049 time to fit residues: 130.8013 Evaluate side-chains 116 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 8 average time/residue: 0.1762 time to fit residues: 4.6480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8494 moved from start: 0.3045 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= 0.186 Angle : 0.471 7.475 19475 Z= 0.249 Chirality : 0.039 0.157 2150 Planarity : 0.003 0.034 2435 Dihedral : 3.745 13.097 1880 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.40 % Allowed : 11.18 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1680 helix: 1.17 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.63 (0.26), residues: 490 *********************** 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 158 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 106 time to evaluate : 1.641 Fit side-chains outliers start: 52 outliers final: 28 residues processed: 135 average time/residue: 0.8429 time to fit residues: 131.3397 Evaluate side-chains 131 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 15 residues processed: 14 average time/residue: 0.2251 time to fit residues: 6.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 73 optimal weight: 0.1980 chunk 98 optimal weight: 0.0770 overall best weight: 2.0544 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.3107 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= 0.194 Angle : 0.480 8.546 19475 Z= 0.255 Chirality : 0.039 0.191 2150 Planarity : 0.003 0.034 2435 Dihedral : 3.684 13.092 1880 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 11.57 % 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: 0.63 (0.20), residues: 1680 helix: 1.23 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 480 *********************** 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 145 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 1.582 Fit side-chains outliers start: 41 outliers final: 23 residues processed: 126 average time/residue: 0.8324 time to fit residues: 121.5562 Evaluate side-chains 125 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.1446 time to fit residues: 4.2409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.8466 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14320 Z= 0.151 Angle : 0.452 8.256 19475 Z= 0.240 Chirality : 0.038 0.155 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.595 13.158 1880 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.48 % Allowed : 11.96 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1680 helix: 1.38 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.58 (0.26), residues: 480 *********************** 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 143 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 105 time to evaluate : 1.801 Fit side-chains outliers start: 38 outliers final: 28 residues processed: 127 average time/residue: 0.8315 time to fit residues: 122.5669 Evaluate side-chains 130 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 16 residues processed: 13 average time/residue: 0.2454 time to fit residues: 6.9471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14320 Z= 0.192 Angle : 0.471 6.602 19475 Z= 0.248 Chirality : 0.039 0.156 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.601 14.252 1880 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.70 % Allowed : 12.94 % Favored : 85.36 % 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: 0.88 (0.21), residues: 1680 helix: 1.41 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 480 *********************** 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 123 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.773 Fit side-chains outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.8854 time to fit residues: 119.8610 Evaluate side-chains 115 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.6712 time to fit residues: 3.8188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8470 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14320 Z= 0.163 Angle : 0.455 8.550 19475 Z= 0.241 Chirality : 0.039 0.155 2150 Planarity : 0.003 0.035 2435 Dihedral : 3.567 13.748 1880 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.70 % Allowed : 13.14 % Favored : 85.16 % 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: 0.98 (0.21), residues: 1680 helix: 1.49 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.51 (0.26), residues: 480 ********************** 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 127 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.633 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 122 average time/residue: 0.8354 time to fit residues: 118.1314 Evaluate side-chains 117 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.1695 time to fit residues: 3.0343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 0.0040 chunk 54 optimal weight: 0.6980 chunk 134 optimal weight: 0.0970 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.100087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.078969 restraints weight = 18530.519| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.45 r_work: 0.2794 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14320 Z= 0.132 Angle : 0.437 5.583 19475 Z= 0.232 Chirality : 0.038 0.154 2150 Planarity : 0.003 0.034 2435 Dihedral : 3.519 13.614 1880 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.76 % Allowed : 12.88 % Favored : 85.36 % 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: 1.13 (0.21), residues: 1680 helix: 1.63 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -1.51 (0.26), residues: 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3586.61 seconds wall clock time: 67 minutes 23.73 seconds (4043.73 seconds total)