Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 12:01:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz7_34391/04_2023/8gz7_34391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz7_34391/04_2023/8gz7_34391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz7_34391/04_2023/8gz7_34391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz7_34391/04_2023/8gz7_34391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz7_34391/04_2023/8gz7_34391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz7_34391/04_2023/8gz7_34391.pdb" } resolution = 3.5 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= 0.017 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 11117 2.51 5 N 3001 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17474 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "C" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "G" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2212 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Chain: "D" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Chain: "F" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 252} Chain breaks: 1 Chain: "H" Number of atoms: 2161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 bond proxies already assigned to first conformer: 2196 Time building chain proxies: 9.36, per 1000 atoms: 0.54 Number of scatterers: 17474 At special positions: 0 Unit cell: (131.56, 126.96, 89.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 3332 8.00 N 3001 7.00 C 11117 6.00 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: 5.80 Conformation dependent library (CDL) restraints added in 2.7 seconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4050 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 29 sheets defined 5.7% alpha, 62.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.583A pdb=" N ARG A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 215 through 220 removed outlier: 3.565A pdb=" N ARG C 219 " --> pdb=" O PRO C 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 207 Processing helix chain 'E' and resid 210 through 214 Processing helix chain 'E' and resid 215 through 220 removed outlier: 3.579A pdb=" N ARG E 219 " --> pdb=" O PRO E 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 207 Processing helix chain 'G' and resid 215 through 220 removed outlier: 3.582A pdb=" N ARG G 219 " --> pdb=" O PRO G 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'H' and resid 186 through 191 Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'H' and resid 198 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 28 removed outlier: 3.703A pdb=" N TYR A 20 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP A 44 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS A 49 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 99 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 231 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL A 97 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 154 removed outlier: 8.618A pdb=" N ALA A 81 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 74 " --> pdb=" O TRP A 257 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TRP A 257 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS A 76 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 255 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR A 78 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 253 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLY A 80 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 251 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 82 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A 252 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN A 269 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN A 254 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR A 267 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ARG A 256 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ALA A 265 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 292 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 280 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU A 290 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP A 282 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 118 removed outlier: 8.433A pdb=" N GLU A 108 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS A 146 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N SER B 102 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN B 138 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU C 108 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS C 146 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR C 142 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N SER D 102 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN D 138 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU E 108 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS E 146 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR E 142 " --> pdb=" O GLN E 112 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 139 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR F 111 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N SER F 102 " --> pdb=" O ASN F 138 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN F 138 " --> pdb=" O SER F 102 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLU G 108 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS G 146 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N SER H 102 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASN H 138 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 28 removed outlier: 3.502A pdb=" N THR C 18 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR C 20 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP C 44 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS C 49 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 99 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER C 231 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL C 97 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 154 removed outlier: 8.565A pdb=" N ALA C 81 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE C 74 " --> pdb=" O TRP C 257 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TRP C 257 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS C 76 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 255 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR C 78 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR C 253 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY C 80 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP C 251 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 252 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN C 269 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLN C 254 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR C 267 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ARG C 256 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ALA C 265 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 292 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLU C 280 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU C 290 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP C 282 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 18 through 28 removed outlier: 3.663A pdb=" N TYR E 20 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 99 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER E 231 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL E 97 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 150 through 154 removed outlier: 8.597A pdb=" N ALA E 81 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE E 74 " --> pdb=" O TRP E 257 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TRP E 257 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS E 76 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE E 255 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR E 78 " --> pdb=" O TYR E 253 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR E 253 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY E 80 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP E 251 " --> pdb=" O GLY E 80 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU E 252 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN E 269 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLN E 254 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N TYR E 267 " --> pdb=" O GLN E 254 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG E 256 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA E 265 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 292 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU E 280 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU E 290 " --> pdb=" O GLU E 280 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 282 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL E 288 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 18 through 28 removed outlier: 3.526A pdb=" N TYR G 20 " --> pdb=" O PHE G 41 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 226 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP G 99 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER G 231 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL G 97 " --> pdb=" O SER G 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 150 through 154 removed outlier: 8.574A pdb=" N ALA G 81 " --> pdb=" O ALA G 169 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE G 74 " --> pdb=" O TRP G 257 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TRP G 257 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS G 76 " --> pdb=" O ILE G 255 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 255 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR G 78 " --> pdb=" O TYR G 253 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR G 253 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLY G 80 " --> pdb=" O ASP G 251 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP G 251 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU G 252 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN G 269 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLN G 254 " --> pdb=" O TYR G 267 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR G 267 " --> pdb=" O GLN G 254 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ARG G 256 " --> pdb=" O ALA G 265 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ALA G 265 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP G 292 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU G 280 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU G 290 " --> pdb=" O GLU G 280 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP G 282 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL G 288 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 13 through 22 removed outlier: 3.911A pdb=" N ALA B 45 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 210 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B 94 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 212 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 13 through 22 removed outlier: 3.911A pdb=" N ALA B 45 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 62 removed outlier: 8.557A pdb=" N PHE B 76 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS B 155 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 59 through 62 removed outlier: 5.335A pdb=" N ARG B 71 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA B 238 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE B 73 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 236 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP B 234 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET B 233 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS B 255 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA B 235 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 253 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N TYR B 237 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N HIS B 251 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N TYR B 239 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N ARG B 249 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR B 241 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N VAL B 247 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 276 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU B 264 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE B 274 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN B 266 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 272 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AB6, first strand: chain 'D' and resid 13 through 22 removed outlier: 3.829A pdb=" N ALA D 45 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER D 214 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU D 91 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 13 through 22 removed outlier: 3.829A pdb=" N ALA D 45 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 59 through 62 removed outlier: 8.531A pdb=" N PHE D 76 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS D 155 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 59 through 62 removed outlier: 5.284A pdb=" N ARG D 71 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA D 238 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE D 73 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR D 236 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP D 234 " --> pdb=" O PRO D 75 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET D 233 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS D 255 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA D 235 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA D 253 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N TYR D 237 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N HIS D 251 " --> pdb=" O TYR D 237 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N TYR D 239 " --> pdb=" O ARG D 249 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N ARG D 249 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N THR D 241 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL D 247 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU D 264 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE D 274 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASN D 266 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL D 272 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AC2, first strand: chain 'F' and resid 13 through 22 removed outlier: 3.841A pdb=" N ALA F 45 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER F 214 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU F 91 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 13 through 22 removed outlier: 3.841A pdb=" N ALA F 45 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 59 through 62 removed outlier: 8.557A pdb=" N PHE F 76 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS F 155 " --> pdb=" O GLU F 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 62 removed outlier: 5.320A pdb=" N ARG F 71 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA F 238 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE F 73 " --> pdb=" O THR F 236 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR F 236 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP F 234 " --> pdb=" O PRO F 75 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET F 233 " --> pdb=" O LYS F 255 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS F 255 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA F 235 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA F 253 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N TYR F 237 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N HIS F 251 " --> pdb=" O TYR F 237 " (cutoff:3.500A) removed outlier: 12.491A pdb=" N TYR F 239 " --> pdb=" O ARG F 249 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N ARG F 249 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N THR F 241 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N VAL F 247 " --> pdb=" O THR F 241 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 276 " --> pdb=" O LYS F 262 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU F 264 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE F 274 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN F 266 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL F 272 " --> pdb=" O ASN F 266 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.513A pdb=" N GLY F 168 " --> pdb=" O THR F 165 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 13 through 22 removed outlier: 3.907A pdb=" N ALA H 45 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE H 210 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER H 214 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU H 91 " --> pdb=" O SER H 214 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 13 through 22 removed outlier: 3.907A pdb=" N ALA H 45 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 59 through 62 removed outlier: 8.555A pdb=" N PHE H 76 " --> pdb=" O ALA H 160 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS H 155 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 59 through 62 removed outlier: 5.289A pdb=" N ARG H 71 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA H 238 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE H 73 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR H 236 " --> pdb=" O ILE H 73 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP H 234 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET H 233 " --> pdb=" O LYS H 255 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS H 255 " --> pdb=" O MET H 233 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA H 235 " --> pdb=" O ALA H 253 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA H 253 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N TYR H 237 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N HIS H 251 " --> pdb=" O TYR H 237 " (cutoff:3.500A) removed outlier: 12.438A pdb=" N TYR H 239 " --> pdb=" O ARG H 249 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N ARG H 249 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 10.559A pdb=" N THR H 241 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N VAL H 247 " --> pdb=" O THR H 241 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER H 276 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU H 264 " --> pdb=" O ILE H 274 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE H 274 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN H 266 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL H 272 " --> pdb=" O ASN H 266 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 162 through 164 837 hydrogen bonds defined for protein. 2298 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: 5.42 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2960 1.32 - 1.44: 5080 1.44 - 1.57: 9801 1.57 - 1.69: 2 1.69 - 1.81: 48 Bond restraints: 17891 Sorted by residual: bond pdb=" C LYS H 3 " pdb=" O LYS H 3 " ideal model delta sigma weight residual 1.231 1.407 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" CA SER D 203 " pdb=" CB SER D 203 " ideal model delta sigma weight residual 1.535 1.484 0.051 1.19e-02 7.06e+03 1.84e+01 bond pdb=" N ILE F 7 " pdb=" CA ILE F 7 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N ILE D 92 " pdb=" CA ILE D 92 " ideal model delta sigma weight residual 1.456 1.490 -0.034 9.50e-03 1.11e+04 1.24e+01 bond pdb=" CA SER B 208 " pdb=" CB SER B 208 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.13e-02 7.83e+03 1.24e+01 ... (remaining 17886 not shown) Histogram of bond angle deviations from ideal: 97.59 - 105.11: 331 105.11 - 112.64: 8341 112.64 - 120.16: 8944 120.16 - 127.68: 6388 127.68 - 135.21: 173 Bond angle restraints: 24177 Sorted by residual: angle pdb=" O LYS H 3 " pdb=" C LYS H 3 " pdb=" CA BLYS H 3 " ideal model delta sigma weight residual 120.80 135.21 -14.41 1.70e+00 3.46e-01 7.18e+01 angle pdb=" O LYS H 3 " pdb=" C LYS H 3 " pdb=" CA ALYS H 3 " ideal model delta sigma weight residual 120.80 135.18 -14.38 1.70e+00 3.46e-01 7.15e+01 angle pdb=" N GLY A 176 " pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 115.80 103.63 12.17 1.74e+00 3.30e-01 4.89e+01 angle pdb=" N GLY E 176 " pdb=" CA GLY E 176 " pdb=" C GLY E 176 " ideal model delta sigma weight residual 115.46 104.26 11.20 1.63e+00 3.76e-01 4.72e+01 angle pdb=" CA GLY D 168 " pdb=" C GLY D 168 " pdb=" O GLY D 168 " ideal model delta sigma weight residual 122.23 117.61 4.62 6.90e-01 2.10e+00 4.48e+01 ... (remaining 24172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.91: 9001 25.91 - 51.82: 1298 51.82 - 77.73: 351 77.73 - 103.65: 10 103.65 - 129.56: 11 Dihedral angle restraints: 10671 sinusoidal: 4360 harmonic: 6311 Sorted by residual: dihedral pdb=" CA GLY A 178 " pdb=" C GLY A 178 " pdb=" N PRO A 179 " pdb=" CA PRO A 179 " ideal model delta harmonic sigma weight residual -180.00 -50.44 -129.56 0 5.00e+00 4.00e-02 6.71e+02 dihedral pdb=" CA GLY C 178 " pdb=" C GLY C 178 " pdb=" N PRO C 179 " pdb=" CA PRO C 179 " ideal model delta harmonic sigma weight residual 180.00 52.29 127.71 0 5.00e+00 4.00e-02 6.52e+02 dihedral pdb=" CA GLY E 178 " pdb=" C GLY E 178 " pdb=" N PRO E 179 " pdb=" CA PRO E 179 " ideal model delta harmonic sigma weight residual -180.00 -52.48 -127.52 0 5.00e+00 4.00e-02 6.50e+02 ... (remaining 10668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 1753 0.137 - 0.275: 734 0.275 - 0.412: 56 0.412 - 0.549: 0 0.549 - 0.686: 2 Chirality restraints: 2545 Sorted by residual: chirality pdb=" CA PRO H 96 " pdb=" N PRO H 96 " pdb=" C PRO H 96 " pdb=" CB PRO H 96 " both_signs ideal model delta sigma weight residual False 2.72 2.03 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA ASN H 167 " pdb=" N ASN H 167 " pdb=" C ASN H 167 " pdb=" CB ASN H 167 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA BLYS H 3 " pdb=" N LYS H 3 " pdb=" C LYS H 3 " pdb=" CB BLYS H 3 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 2542 not shown) Planarity restraints: 3113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H 278 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C THR H 278 " -0.054 2.00e-02 2.50e+03 pdb=" O THR H 278 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO H 279 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 278 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C THR B 278 " -0.052 2.00e-02 2.50e+03 pdb=" O THR B 278 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO B 279 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 71 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C ASP A 71 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 71 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 72 " 0.015 2.00e-02 2.50e+03 ... (remaining 3110 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 6 2.33 - 2.98: 8339 2.98 - 3.62: 22588 3.62 - 4.26: 43844 4.26 - 4.90: 71766 Nonbonded interactions: 146543 Sorted by model distance: nonbonded pdb=" O ASP A 235 " pdb=" OD1 ASP A 235 " model vdw 1.693 3.040 nonbonded pdb=" NH2 ARG A 233 " pdb=" OD1 ASP A 235 " model vdw 1.774 2.520 nonbonded pdb=" CA LYS A 49 " pdb=" NE2 GLN A 234 " model vdw 1.962 3.550 nonbonded pdb=" N LYS A 49 " pdb=" NE2 GLN A 234 " model vdw 2.056 3.200 nonbonded pdb=" O ASP A 48 " pdb=" NE2 GLN A 234 " model vdw 2.065 2.520 ... (remaining 146538 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 4 through 280) selection = (chain 'D' and resid 4 through 280) selection = (chain 'F' and resid 4 through 280) selection = (chain 'H' and resid 4 through 280) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.750 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 43.540 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.012 0.176 17891 Z= 0.792 Angle : 1.671 17.053 24177 Z= 1.209 Chirality : 0.130 0.686 2545 Planarity : 0.005 0.031 3113 Dihedral : 24.080 129.557 6621 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.80 % Favored : 93.49 % Rotamer Outliers : 32.81 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 15.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2104 helix: -3.38 (0.58), residues: 24 sheet: -0.17 (0.15), residues: 1172 loop : -1.49 (0.17), residues: 908 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 627 poor density : 510 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 627 outliers final: 90 residues processed: 912 average time/residue: 0.3744 time to fit residues: 472.4874 Evaluate side-chains 284 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 194 time to evaluate : 2.098 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 90 outliers final: 5 residues processed: 90 average time/residue: 0.2121 time to fit residues: 34.4007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 113 ASN A 144 ASN A 266 ASN A 298 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 110 GLN C 206 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN E 70 ASN ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN G 113 ASN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 GLN G 266 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 107 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 167 ASN D 266 ASN F 150 ASN F 167 ASN F 243 HIS H 107 GLN H 130 ASN H 141 ASN ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17891 Z= 0.218 Angle : 0.643 6.866 24177 Z= 0.356 Chirality : 0.047 0.391 2545 Planarity : 0.005 0.084 3113 Dihedral : 6.555 89.456 2349 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.95 % Allowed : 3.75 % Favored : 95.29 % Rotamer Outliers : 4.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 13.89 % 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: -0.49 (0.18), residues: 2104 helix: -2.80 (0.57), residues: 48 sheet: 0.35 (0.15), residues: 1212 loop : -1.12 (0.19), residues: 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 182 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 35 residues processed: 254 average time/residue: 0.2893 time to fit residues: 112.7917 Evaluate side-chains 175 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1712 time to fit residues: 13.6494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 234 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN G 247 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN H 29 GLN H 77 GLN ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 17891 Z= 0.484 Angle : 0.722 8.634 24177 Z= 0.398 Chirality : 0.052 0.325 2545 Planarity : 0.005 0.083 3113 Dihedral : 6.428 83.091 2349 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.56 % Favored : 94.96 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 13.89 % 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: -0.66 (0.18), residues: 2104 helix: -2.87 (0.79), residues: 24 sheet: 0.26 (0.15), residues: 1192 loop : -1.31 (0.19), residues: 888 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 130 time to evaluate : 2.173 Fit side-chains outliers start: 65 outliers final: 45 residues processed: 190 average time/residue: 0.3200 time to fit residues: 92.7952 Evaluate side-chains 157 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 2.138 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.1603 time to fit residues: 16.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN F 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 17891 Z= 0.158 Angle : 0.538 7.304 24177 Z= 0.294 Chirality : 0.045 0.283 2545 Planarity : 0.004 0.068 3113 Dihedral : 5.798 78.817 2349 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 2.47 % Favored : 97.05 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.10 % 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: -0.41 (0.18), residues: 2104 helix: -2.83 (0.65), residues: 48 sheet: 0.48 (0.15), residues: 1192 loop : -1.15 (0.19), residues: 864 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 2.219 Fit side-chains outliers start: 25 outliers final: 8 residues processed: 150 average time/residue: 0.3460 time to fit residues: 76.6334 Evaluate side-chains 119 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1537 time to fit residues: 5.2633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 17891 Z= 0.364 Angle : 0.593 6.187 24177 Z= 0.326 Chirality : 0.048 0.265 2545 Planarity : 0.005 0.075 3113 Dihedral : 5.855 77.484 2349 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.42 % Favored : 95.10 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % 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: -0.43 (0.18), residues: 2104 helix: -3.17 (0.75), residues: 24 sheet: 0.40 (0.15), residues: 1192 loop : -1.11 (0.19), residues: 888 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 2.299 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 134 average time/residue: 0.3320 time to fit residues: 67.3473 Evaluate side-chains 129 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1640 time to fit residues: 8.0594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 17891 Z= 0.351 Angle : 0.576 5.581 24177 Z= 0.317 Chirality : 0.047 0.257 2545 Planarity : 0.005 0.077 3113 Dihedral : 5.809 75.589 2349 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.18 % Favored : 95.34 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % 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: -0.47 (0.18), residues: 2104 helix: -3.36 (0.78), residues: 24 sheet: 0.32 (0.15), residues: 1192 loop : -1.06 (0.19), residues: 888 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 2.248 Fit side-chains outliers start: 35 outliers final: 16 residues processed: 141 average time/residue: 0.3309 time to fit residues: 70.3555 Evaluate side-chains 127 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 2.138 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1606 time to fit residues: 7.7838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17891 Z= 0.246 Angle : 0.533 8.487 24177 Z= 0.291 Chirality : 0.046 0.241 2545 Planarity : 0.004 0.075 3113 Dihedral : 5.591 74.103 2349 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.56 % Favored : 95.06 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % 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: -0.38 (0.18), residues: 2104 helix: -3.30 (0.81), residues: 24 sheet: 0.38 (0.15), residues: 1192 loop : -0.99 (0.19), residues: 888 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 2.180 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 129 average time/residue: 0.3452 time to fit residues: 66.8049 Evaluate side-chains 124 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2000 time to fit residues: 8.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 17891 Z= 0.319 Angle : 0.560 7.184 24177 Z= 0.306 Chirality : 0.047 0.229 2545 Planarity : 0.005 0.079 3113 Dihedral : 5.631 73.425 2349 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.47 % Favored : 95.10 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % 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: -0.43 (0.18), residues: 2104 helix: -3.42 (0.78), residues: 24 sheet: 0.35 (0.16), residues: 1192 loop : -1.03 (0.19), residues: 888 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 2.207 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.3381 time to fit residues: 65.2204 Evaluate side-chains 122 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1660 time to fit residues: 6.2700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.0470 chunk 178 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17891 Z= 0.178 Angle : 0.509 7.667 24177 Z= 0.277 Chirality : 0.045 0.215 2545 Planarity : 0.004 0.075 3113 Dihedral : 5.376 75.282 2349 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.42 % Favored : 96.25 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % 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: -0.27 (0.18), residues: 2104 helix: -3.08 (0.68), residues: 48 sheet: 0.48 (0.15), residues: 1216 loop : -0.93 (0.20), residues: 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 2.240 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 0.3345 time to fit residues: 56.0782 Evaluate side-chains 103 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1512 time to fit residues: 4.0432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 95 optimal weight: 0.0770 chunk 139 optimal weight: 9.9990 chunk 211 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 overall best weight: 3.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 17891 Z= 0.290 Angle : 0.542 7.145 24177 Z= 0.296 Chirality : 0.046 0.211 2545 Planarity : 0.004 0.079 3113 Dihedral : 5.491 77.148 2349 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.66 % Favored : 94.91 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % 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: -0.30 (0.18), residues: 2104 helix: -3.37 (0.81), residues: 24 sheet: 0.39 (0.15), residues: 1224 loop : -0.92 (0.20), residues: 856 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 2.119 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.3529 time to fit residues: 60.2754 Evaluate side-chains 110 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2039 time to fit residues: 3.8273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** 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 = 0.3661 r_free = 0.3661 target = 0.128922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107474 restraints weight = 43185.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112432 restraints weight = 17639.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115706 restraints weight = 9901.874| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17891 Z= 0.199 Angle : 0.513 7.395 24177 Z= 0.279 Chirality : 0.045 0.195 2545 Planarity : 0.004 0.079 3113 Dihedral : 5.374 76.809 2349 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.80 % Favored : 95.87 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 9.72 % 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: -0.27 (0.19), residues: 2104 helix: -3.14 (0.66), residues: 48 sheet: 0.47 (0.15), residues: 1216 loop : -0.89 (0.20), residues: 840 =============================================================================== Job complete usr+sys time: 3163.75 seconds wall clock time: 59 minutes 26.07 seconds (3566.07 seconds total)