Starting phenix.real_space_refine (version: dev) on Fri May 13 09:41:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/05_2022/6kpe_0743.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/05_2022/6kpe_0743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/05_2022/6kpe_0743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/05_2022/6kpe_0743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/05_2022/6kpe_0743.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/05_2022/6kpe_0743.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.007 sd= 0.312 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 62184 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "B" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "C" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "F" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "G" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "K" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "L" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.43, per 1000 atoms: 0.33 Number of scatterers: 62184 At special positions: 0 Unit cell: (143.64, 143.64, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 Mg 12 11.99 O 5760 8.00 N 5076 7.00 C 20004 6.00 H 31212 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 37.50 Conformation dependent library (CDL) restraints added in 3.7 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 12 sheets defined 64.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.749A pdb=" N MET A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 254 through 286 removed outlier: 5.826A pdb=" N ASP A 270 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP B 270 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 271 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.656A pdb=" N GLU C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 217 removed outlier: 3.583A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP C 270 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 271 " --> pdb=" O LYS C 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP D 270 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 48 through 56 removed outlier: 3.656A pdb=" N GLU E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 139 " --> pdb=" O GLY E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 217 removed outlier: 3.583A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 244 Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP E 270 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 271 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY E 286 " --> pdb=" O TYR E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 85 through 91 Processing helix chain 'F' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET F 137 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 139 " --> pdb=" O GLY F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL F 271 " --> pdb=" O LYS F 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY F 286 " --> pdb=" O TYR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 313 through 326 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 48 through 56 removed outlier: 3.656A pdb=" N GLU G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 71 Processing helix chain 'G' and resid 85 through 91 Processing helix chain 'G' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 133 through 143 removed outlier: 3.749A pdb=" N MET G 137 " --> pdb=" O GLY G 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 139 " --> pdb=" O GLY G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 217 removed outlier: 3.583A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 244 Processing helix chain 'G' and resid 247 through 253 Processing helix chain 'G' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP G 270 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL G 271 " --> pdb=" O LYS G 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 286 " --> pdb=" O TYR G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 Processing helix chain 'G' and resid 300 through 312 Processing helix chain 'G' and resid 313 through 326 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 85 through 91 Processing helix chain 'H' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET H 137 " --> pdb=" O GLY H 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 139 " --> pdb=" O GLY H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.616A pdb=" N GLU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 244 Processing helix chain 'H' and resid 247 through 253 Processing helix chain 'H' and resid 254 through 286 removed outlier: 5.826A pdb=" N ASP H 270 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL H 271 " --> pdb=" O LYS H 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 Processing helix chain 'H' and resid 300 through 312 Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU I 52 " --> pdb=" O ASP I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 85 through 91 Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET I 137 " --> pdb=" O GLY I 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU I 139 " --> pdb=" O GLY I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU I 187 " --> pdb=" O SER I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA I 224 " --> pdb=" O SER I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 244 Processing helix chain 'I' and resid 247 through 253 Processing helix chain 'I' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL I 271 " --> pdb=" O LYS I 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY I 286 " --> pdb=" O TYR I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 Processing helix chain 'I' and resid 300 through 312 Processing helix chain 'I' and resid 313 through 326 Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU J 52 " --> pdb=" O ASP J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 85 through 91 Processing helix chain 'J' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU J 139 " --> pdb=" O GLY J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.616A pdb=" N GLU J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 244 Processing helix chain 'J' and resid 247 through 253 Processing helix chain 'J' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP J 270 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL J 271 " --> pdb=" O LYS J 267 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY J 286 " --> pdb=" O TYR J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 Processing helix chain 'J' and resid 300 through 312 Processing helix chain 'J' and resid 313 through 326 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 85 through 91 Processing helix chain 'K' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET K 137 " --> pdb=" O GLY K 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 139 " --> pdb=" O GLY K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 244 Processing helix chain 'K' and resid 247 through 253 Processing helix chain 'K' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP K 270 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL K 271 " --> pdb=" O LYS K 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY K 286 " --> pdb=" O TYR K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 Processing helix chain 'K' and resid 300 through 312 Processing helix chain 'K' and resid 313 through 326 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU L 52 " --> pdb=" O ASP L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 71 Processing helix chain 'L' and resid 85 through 91 Processing helix chain 'L' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET L 137 " --> pdb=" O GLY L 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU L 139 " --> pdb=" O GLY L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 244 Processing helix chain 'L' and resid 247 through 253 Processing helix chain 'L' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP L 270 " --> pdb=" O PHE L 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL L 271 " --> pdb=" O LYS L 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY L 286 " --> pdb=" O TYR L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 Processing helix chain 'L' and resid 300 through 312 Processing helix chain 'L' and resid 313 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 7.271A pdb=" N VAL A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA A 74 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 42 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL B 148 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 74 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 42 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 removed outlier: 7.271A pdb=" N VAL C 148 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE C 105 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 74 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 42 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL D 148 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA D 74 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 42 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 7.269A pdb=" N VAL E 148 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA E 74 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE E 42 " --> pdb=" O ILE E 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL F 148 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 74 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 42 " --> pdb=" O ILE F 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL G 148 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA G 74 " --> pdb=" O ASP G 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 42 " --> pdb=" O ILE G 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL H 148 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA H 74 " --> pdb=" O ASP H 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 42 " --> pdb=" O ILE H 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL I 148 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA I 74 " --> pdb=" O ASP I 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE I 42 " --> pdb=" O ILE I 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL J 148 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE J 105 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA J 74 " --> pdb=" O ASP J 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE J 42 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL K 148 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA K 74 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE K 42 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL L 148 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE L 105 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA L 74 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE L 42 " --> pdb=" O ILE L 18 " (cutoff:3.500A) 1788 hydrogen bonds defined for protein. 5184 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: 19.23 Time building geometry restraints manager: 39.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 31198 1.02 - 1.22: 14 1.22 - 1.41: 12993 1.41 - 1.61: 18375 1.61 - 1.80: 228 Bond restraints: 62808 Sorted by residual: bond pdb=" CB SER E 121 " pdb=" HB3 SER E 121 " ideal model delta sigma weight residual 0.970 1.064 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CB SER E 121 " pdb=" HB2 SER E 121 " ideal model delta sigma weight residual 0.970 1.025 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" OG SER E 121 " pdb=" HG SER E 121 " ideal model delta sigma weight residual 0.840 0.885 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" CB SER H 121 " pdb=" HB2 SER H 121 " ideal model delta sigma weight residual 0.970 1.006 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" CB ASP K 80 " pdb=" HB2 ASP K 80 " ideal model delta sigma weight residual 0.970 1.005 -0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 62803 not shown) Histogram of bond angle deviations from ideal: 70.08 - 83.31: 311 83.31 - 96.55: 47 96.55 - 109.78: 48252 109.78 - 123.01: 59156 123.01 - 136.25: 6186 Bond angle restraints: 113952 Sorted by residual: angle pdb=" CG2 VAL C 68 " pdb=" CB VAL C 68 " pdb=" HB VAL C 68 " ideal model delta sigma weight residual 108.00 70.08 37.92 3.00e+00 1.11e-01 1.60e+02 angle pdb=" CG2 ILE G 171 " pdb=" CB ILE G 171 " pdb=" HB ILE G 171 " ideal model delta sigma weight residual 109.00 71.41 37.59 3.00e+00 1.11e-01 1.57e+02 angle pdb=" CG1 ILE J 174 " pdb=" CB ILE J 174 " pdb=" HB ILE J 174 " ideal model delta sigma weight residual 109.00 71.94 37.06 3.00e+00 1.11e-01 1.53e+02 angle pdb=" CG1 ILE I 178 " pdb=" CB ILE I 178 " pdb=" HB ILE I 178 " ideal model delta sigma weight residual 109.00 71.97 37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CG1 ILE G 171 " pdb=" CB ILE G 171 " pdb=" HB ILE G 171 " ideal model delta sigma weight residual 109.00 72.20 36.80 3.00e+00 1.11e-01 1.50e+02 ... (remaining 113947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 22312 17.51 - 35.03: 2119 35.03 - 52.54: 321 52.54 - 70.05: 74 70.05 - 87.57: 14 Dihedral angle restraints: 24840 sinusoidal: 11484 harmonic: 13356 Sorted by residual: dihedral pdb=" CA LYS B 14 " pdb=" C LYS B 14 " pdb=" N GLY B 15 " pdb=" CA GLY B 15 " ideal model delta harmonic sigma weight residual -180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LYS L 14 " pdb=" C LYS L 14 " pdb=" N GLY L 15 " pdb=" CA GLY L 15 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LYS G 14 " pdb=" C LYS G 14 " pdb=" N GLY G 15 " pdb=" CA GLY G 15 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 24837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.322: 4632 0.322 - 0.645: 0 0.645 - 0.967: 0 0.967 - 1.289: 0 1.289 - 1.612: 36 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CB VAL B 29 " pdb=" CA VAL B 29 " pdb=" CG1 VAL B 29 " pdb=" CG2 VAL B 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" CB VAL C 29 " pdb=" CA VAL C 29 " pdb=" CG1 VAL C 29 " pdb=" CG2 VAL C 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" CB VAL F 29 " pdb=" CA VAL F 29 " pdb=" CG1 VAL F 29 " pdb=" CG2 VAL F 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.61 2.00e-01 2.50e+01 6.49e+01 ... (remaining 4665 not shown) Planarity restraints: 9204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 128 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO A 129 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 128 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO E 129 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 128 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO J 129 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO J 129 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 129 " -0.025 5.00e-02 4.00e+02 ... (remaining 9201 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2785 2.13 - 2.75: 121437 2.75 - 3.37: 172163 3.37 - 3.98: 223179 3.98 - 4.60: 360445 Nonbonded interactions: 880009 Sorted by model distance: nonbonded pdb=" OE1 GLU E 222 " pdb=" H GLU E 222 " model vdw 1.514 1.850 nonbonded pdb=" OE1 GLU A 222 " pdb=" H GLU A 222 " model vdw 1.514 1.850 nonbonded pdb=" OE1 GLU D 222 " pdb=" H GLU D 222 " model vdw 1.515 1.850 nonbonded pdb=" OE1 GLU B 222 " pdb=" H GLU B 222 " model vdw 1.515 1.850 nonbonded pdb=" OE1 GLU H 222 " pdb=" H GLU H 222 " model vdw 1.515 1.850 ... (remaining 880004 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 12 5.21 5 S 120 5.16 5 C 20004 2.51 5 N 5076 2.21 5 O 5760 1.98 5 H 31212 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.660 Extract box with map and model: 12.530 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.400 Process input model: 137.090 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.009 0.042 31596 Z= 0.566 Angle : 0.818 11.350 42660 Z= 0.446 Chirality : 0.142 1.612 4668 Planarity : 0.004 0.046 5424 Dihedral : 13.073 67.361 11736 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -5.24 (0.10), residues: 3912 helix: -3.06 (0.08), residues: 2172 sheet: -4.07 (0.21), residues: 264 loop : -3.79 (0.13), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 609 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 609 average time/residue: 2.9012 time to fit residues: 2041.7842 Evaluate side-chains 377 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 3.718 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.6980 chunk 291 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 196 optimal weight: 0.0070 chunk 155 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 0.6980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 249 GLN A 278 ASN A 296 GLN B 96 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 278 ASN B 296 GLN C 96 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 249 GLN C 278 ASN C 296 GLN D 96 GLN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 249 GLN D 278 ASN D 296 GLN E 96 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN E 278 ASN E 296 GLN F 96 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN F 249 GLN F 278 ASN F 296 GLN G 96 GLN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 GLN G 249 GLN G 278 ASN G 296 GLN H 96 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN H 249 GLN H 278 ASN H 296 GLN I 96 GLN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN I 249 GLN I 278 ASN I 296 GLN J 96 GLN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 GLN J 249 GLN J 278 ASN J 296 GLN K 96 GLN ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN K 278 ASN K 296 GLN L 96 GLN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN L 249 GLN L 278 ASN L 296 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 31596 Z= 0.221 Angle : 0.778 15.854 42660 Z= 0.400 Chirality : 0.156 1.708 4668 Planarity : 0.004 0.042 5424 Dihedral : 5.173 20.975 4284 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.87 (0.12), residues: 3912 helix: -0.98 (0.10), residues: 2292 sheet: -3.11 (0.17), residues: 408 loop : -3.06 (0.16), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 433 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 18 residues processed: 465 average time/residue: 2.5848 time to fit residues: 1412.2731 Evaluate side-chains 387 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 369 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 10 average time/residue: 1.6179 time to fit residues: 25.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 ASN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 ASN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 31596 Z= 0.363 Angle : 0.808 15.833 42660 Z= 0.416 Chirality : 0.157 1.766 4668 Planarity : 0.004 0.035 5424 Dihedral : 4.991 19.806 4284 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.11 (0.12), residues: 3912 helix: -0.39 (0.10), residues: 2292 sheet: -2.40 (0.19), residues: 408 loop : -2.85 (0.17), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 379 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 52 residues processed: 435 average time/residue: 2.4138 time to fit residues: 1250.2793 Evaluate side-chains 385 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 333 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 36 residues processed: 16 average time/residue: 0.9946 time to fit residues: 27.4411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 31596 Z= 0.285 Angle : 0.754 15.710 42660 Z= 0.383 Chirality : 0.157 1.745 4668 Planarity : 0.003 0.045 5424 Dihedral : 4.803 19.265 4284 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.54 (0.13), residues: 3912 helix: -0.02 (0.10), residues: 2304 sheet: -2.10 (0.20), residues: 408 loop : -2.47 (0.17), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 385 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 50 residues processed: 445 average time/residue: 2.2990 time to fit residues: 1227.2547 Evaluate side-chains 393 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 343 time to evaluate : 3.713 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 43 residues processed: 8 average time/residue: 0.8172 time to fit residues: 14.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 31596 Z= 0.314 Angle : 0.762 15.891 42660 Z= 0.388 Chirality : 0.158 1.774 4668 Planarity : 0.003 0.035 5424 Dihedral : 4.712 18.862 4284 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3912 helix: 0.13 (0.10), residues: 2316 sheet: -1.89 (0.21), residues: 408 loop : -2.29 (0.18), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 366 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 53 residues processed: 434 average time/residue: 2.2955 time to fit residues: 1197.3515 Evaluate side-chains 390 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 337 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 44 residues processed: 9 average time/residue: 1.0312 time to fit residues: 17.8850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 31596 Z= 0.269 Angle : 0.741 15.472 42660 Z= 0.375 Chirality : 0.157 1.761 4668 Planarity : 0.003 0.053 5424 Dihedral : 4.623 18.158 4284 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3912 helix: 0.28 (0.10), residues: 2328 sheet: -1.74 (0.22), residues: 408 loop : -2.01 (0.18), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 373 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 43 residues processed: 454 average time/residue: 2.3360 time to fit residues: 1282.2995 Evaluate side-chains 379 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 336 time to evaluate : 3.800 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.8126 time to fit residues: 11.1532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 31596 Z= 0.275 Angle : 0.746 15.463 42660 Z= 0.376 Chirality : 0.157 1.768 4668 Planarity : 0.003 0.054 5424 Dihedral : 4.547 17.725 4284 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.13), residues: 3912 helix: 0.41 (0.10), residues: 2316 sheet: -1.58 (0.23), residues: 408 loop : -2.10 (0.18), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 362 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 41 residues processed: 434 average time/residue: 2.2510 time to fit residues: 1180.9650 Evaluate side-chains 383 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 342 time to evaluate : 3.766 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 37 residues processed: 4 average time/residue: 1.7381 time to fit residues: 13.4680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 31596 Z= 0.267 Angle : 0.750 15.500 42660 Z= 0.376 Chirality : 0.157 1.762 4668 Planarity : 0.003 0.056 5424 Dihedral : 4.507 17.267 4284 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.74 (0.13), residues: 3912 helix: 0.49 (0.10), residues: 2328 sheet: -1.53 (0.23), residues: 420 loop : -1.98 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 366 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 41 residues processed: 429 average time/residue: 2.2158 time to fit residues: 1145.1520 Evaluate side-chains 385 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 344 time to evaluate : 3.716 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 40 residues processed: 2 average time/residue: 1.6119 time to fit residues: 8.6807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 8.9990 chunk 354 optimal weight: 8.9990 chunk 323 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 270 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 3.9990 chunk 343 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 142 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 31596 Z= 0.217 Angle : 0.741 15.432 42660 Z= 0.369 Chirality : 0.157 1.752 4668 Planarity : 0.003 0.046 5424 Dihedral : 4.395 16.708 4284 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.48 (0.13), residues: 3912 helix: 0.66 (0.11), residues: 2328 sheet: -1.34 (0.24), residues: 420 loop : -1.82 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 359 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 42 residues processed: 413 average time/residue: 2.3643 time to fit residues: 1178.1101 Evaluate side-chains 384 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 342 time to evaluate : 4.727 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 39 residues processed: 3 average time/residue: 1.7578 time to fit residues: 12.3029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 8.9990 chunk 364 optimal weight: 6.9990 chunk 222 optimal weight: 0.5980 chunk 173 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN C 142 GLN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN J 142 GLN ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 31596 Z= 0.217 Angle : 0.743 15.519 42660 Z= 0.370 Chirality : 0.157 1.763 4668 Planarity : 0.003 0.046 5424 Dihedral : 4.312 15.914 4284 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.33 (0.13), residues: 3912 helix: 0.77 (0.11), residues: 2340 sheet: -1.17 (0.24), residues: 420 loop : -1.81 (0.18), residues: 1152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 355 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 37 residues processed: 402 average time/residue: 2.3512 time to fit residues: 1138.3803 Evaluate side-chains 371 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 334 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 36 residues processed: 1 average time/residue: 1.6449 time to fit residues: 6.7165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.097168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072598 restraints weight = 245801.654| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.73 r_work: 0.3085 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work: 0.3055 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work: 0.3041 rms_B_bonded: 3.52 restraints_weight: 0.0625 r_work: 0.3026 rms_B_bonded: 3.61 restraints_weight: 0.0312 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.0156 r_work: 0.2994 rms_B_bonded: 3.90 restraints_weight: 0.0078 r_work: 0.2977 rms_B_bonded: 4.09 restraints_weight: 0.0039 r_work: 0.2960 rms_B_bonded: 4.32 restraints_weight: 0.0020 r_work: 0.2941 rms_B_bonded: 4.59 restraints_weight: 0.0010 r_work: 0.2922 rms_B_bonded: 4.89 restraints_weight: 0.0005 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 31596 Z= 0.252 Angle : 0.753 15.472 42660 Z= 0.376 Chirality : 0.157 1.763 4668 Planarity : 0.003 0.052 5424 Dihedral : 4.293 15.607 4284 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.13), residues: 3912 helix: 0.75 (0.11), residues: 2340 sheet: -1.11 (0.24), residues: 420 loop : -1.74 (0.18), residues: 1152 =============================================================================== Job complete usr+sys time: 17571.81 seconds wall clock time: 302 minutes 14.16 seconds (18134.16 seconds total)