Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 07:22:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/04_2023/7whr_32509.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/04_2023/7whr_32509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/04_2023/7whr_32509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/04_2023/7whr_32509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/04_2023/7whr_32509.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/04_2023/7whr_32509.pdb" } resolution = 3.4 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= 0.000 sd= 0.027 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 102 5.16 5 C 10842 2.51 5 N 2874 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 374": "OE1" <-> "OE2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16914 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "C" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "D" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "E" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "F" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Time building chain proxies: 9.07, per 1000 atoms: 0.54 Number of scatterers: 16914 At special positions: 0 Unit cell: (128.27, 126.25, 118.17, 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 102 16.00 O 3096 8.00 N 2874 7.00 C 10842 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: 6.71 Conformation dependent library (CDL) restraints added in 2.6 seconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 51 sheets defined 21.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 4.032A pdb=" N LEU B 25 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 41 through 53 removed outlier: 4.327A pdb=" N GLN B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 74 through 81 removed outlier: 5.079A pdb=" N LEU B 79 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY B 80 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 81 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.927A pdb=" N TYR B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 153' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 242 through 245 removed outlier: 3.723A pdb=" N VAL B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.950A pdb=" N LEU A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 33 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 74 through 81 removed outlier: 5.083A pdb=" N LEU A 79 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 80 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 81 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.908A pdb=" N TYR A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 153' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 242 through 245 removed outlier: 3.713A pdb=" N VAL A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'C' and resid 22 through 26 removed outlier: 3.957A pdb=" N LEU C 25 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 Processing helix chain 'C' and resid 41 through 53 removed outlier: 4.315A pdb=" N GLN C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 74 through 81 removed outlier: 5.112A pdb=" N LEU C 79 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY C 80 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 81 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.920A pdb=" N TYR C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY C 153 " --> pdb=" O TRP C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 153' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 201 through 204 removed outlier: 3.990A pdb=" N GLU C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 242 through 245 removed outlier: 3.707A pdb=" N VAL C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 245' Processing helix chain 'D' and resid 22 through 26 removed outlier: 4.034A pdb=" N LEU D 25 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 33 Processing helix chain 'D' and resid 42 through 53 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 74 through 81 removed outlier: 5.101A pdb=" N LEU D 79 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 81 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.940A pdb=" N TYR D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY D 153 " --> pdb=" O TRP D 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 153' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 242 through 245 removed outlier: 3.721A pdb=" N VAL D 245 " --> pdb=" O PRO D 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 242 through 245' Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.961A pdb=" N LEU E 25 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 74 through 81 removed outlier: 5.068A pdb=" N LEU E 79 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY E 80 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 81 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.907A pdb=" N TYR E 152 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY E 153 " --> pdb=" O TRP E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 148 through 153' Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 205 through 212 Processing helix chain 'E' and resid 229 through 241 Processing helix chain 'E' and resid 242 through 245 removed outlier: 3.685A pdb=" N VAL E 245 " --> pdb=" O PRO E 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 242 through 245' Processing helix chain 'F' and resid 22 through 26 removed outlier: 4.020A pdb=" N LEU F 25 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 Processing helix chain 'F' and resid 41 through 53 removed outlier: 4.323A pdb=" N GLN F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 74 through 81 removed outlier: 5.072A pdb=" N LEU F 79 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY F 80 " --> pdb=" O ARG F 77 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL F 81 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.922A pdb=" N TYR F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY F 153 " --> pdb=" O TRP F 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 148 through 153' Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 205 through 212 Processing helix chain 'F' and resid 229 through 241 Processing helix chain 'F' and resid 242 through 245 removed outlier: 3.707A pdb=" N VAL F 245 " --> pdb=" O PRO F 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.649A pdb=" N VAL B 57 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 113 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 180 removed outlier: 4.330A pdb=" N GLN B 145 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.672A pdb=" N VAL B 168 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.902A pdb=" N THR B 268 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 286 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 304 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 274 through 275 removed outlier: 6.833A pdb=" N LEU B 274 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER B 292 " --> pdb=" O ILE B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.385A pdb=" N GLU B 350 " --> pdb=" O VAL B 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.767A pdb=" N LYS B 361 " --> pdb=" O ILE B 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.675A pdb=" N VAL A 57 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 87 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 61 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.675A pdb=" N VAL A 57 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A 113 " --> pdb=" O ARG A 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AB3, first strand: chain 'A' and resid 178 through 180 removed outlier: 4.319A pdb=" N GLN A 145 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 155 through 156 removed outlier: 3.662A pdb=" N VAL A 168 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.968A pdb=" N THR A 268 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 286 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 304 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET A 321 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.862A pdb=" N LEU A 274 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 292 " --> pdb=" O ILE A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 350 through 351 removed outlier: 6.494A pdb=" N GLU A 350 " --> pdb=" O VAL A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.671A pdb=" N LYS A 361 " --> pdb=" O ILE A 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.771A pdb=" N VAL C 57 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE C 113 " --> pdb=" O ARG C 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'C' and resid 178 through 180 removed outlier: 4.280A pdb=" N GLN C 145 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.704A pdb=" N VAL C 168 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.920A pdb=" N THR C 268 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 286 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG C 304 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N MET C 321 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 274 through 275 removed outlier: 6.911A pdb=" N LEU C 274 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER C 292 " --> pdb=" O ILE C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 350 through 351 removed outlier: 6.515A pdb=" N GLU C 350 " --> pdb=" O VAL C 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.775A pdb=" N LYS C 361 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.652A pdb=" N VAL D 57 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL D 87 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU D 59 " --> pdb=" O VAL D 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.652A pdb=" N VAL D 57 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 113 " --> pdb=" O ARG D 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AD2, first strand: chain 'D' and resid 178 through 180 removed outlier: 4.267A pdb=" N GLN D 145 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 155 through 156 removed outlier: 3.672A pdb=" N VAL D 168 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 268 through 269 removed outlier: 6.900A pdb=" N THR D 268 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 286 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG D 304 " --> pdb=" O VAL D 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 274 through 275 removed outlier: 6.835A pdb=" N LEU D 274 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER D 292 " --> pdb=" O ILE D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 350 through 351 removed outlier: 6.384A pdb=" N GLU D 350 " --> pdb=" O VAL D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.766A pdb=" N LYS D 361 " --> pdb=" O ILE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 82 through 83 removed outlier: 3.723A pdb=" N VAL E 57 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL E 87 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL E 61 " --> pdb=" O VAL E 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 82 through 83 removed outlier: 3.723A pdb=" N VAL E 57 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 113 " --> pdb=" O ARG E 10 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AE2, first strand: chain 'E' and resid 178 through 180 removed outlier: 4.309A pdb=" N GLN E 145 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 155 through 156 removed outlier: 3.663A pdb=" N VAL E 168 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 268 through 269 removed outlier: 6.963A pdb=" N THR E 268 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL E 286 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG E 304 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET E 321 " --> pdb=" O ILE E 339 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 274 through 275 removed outlier: 6.868A pdb=" N LEU E 274 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER E 292 " --> pdb=" O ILE E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 350 through 351 removed outlier: 6.494A pdb=" N GLU E 350 " --> pdb=" O VAL E 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.673A pdb=" N LYS E 361 " --> pdb=" O ILE E 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 82 through 83 removed outlier: 3.867A pdb=" N VAL F 57 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA F 11 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA F 60 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE F 13 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE F 113 " --> pdb=" O ARG F 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AF1, first strand: chain 'F' and resid 178 through 180 removed outlier: 4.283A pdb=" N GLN F 145 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 155 through 156 removed outlier: 3.705A pdb=" N VAL F 168 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 268 through 269 removed outlier: 6.920A pdb=" N THR F 268 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL F 286 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG F 304 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N MET F 321 " --> pdb=" O ILE F 339 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 274 through 275 removed outlier: 6.912A pdb=" N LEU F 274 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER F 292 " --> pdb=" O ILE F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 350 through 351 removed outlier: 6.503A pdb=" N GLU F 350 " --> pdb=" O VAL F 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.794A pdb=" N LYS F 361 " --> pdb=" O ILE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 312 hydrogen bonds defined for protein. 756 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: 5.45 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5541 1.34 - 1.46: 2992 1.46 - 1.58: 8567 1.58 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 17274 Sorted by residual: bond pdb=" CG1 ILE A 46 " pdb=" CD1 ILE A 46 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 bond pdb=" CG1 ILE D 46 " pdb=" CD1 ILE D 46 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CG1 ILE E 46 " pdb=" CD1 ILE E 46 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" CA LYS D 170 " pdb=" CB LYS D 170 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.45e+00 bond pdb=" CA LYS E 170 " pdb=" CB LYS E 170 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.40e+00 ... (remaining 17269 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.33: 643 106.33 - 113.26: 9247 113.26 - 120.18: 5822 120.18 - 127.11: 7450 127.11 - 134.04: 214 Bond angle restraints: 23376 Sorted by residual: angle pdb=" CA LEU E 92 " pdb=" CB LEU E 92 " pdb=" CG LEU E 92 " ideal model delta sigma weight residual 116.30 127.18 -10.88 3.50e+00 8.16e-02 9.67e+00 angle pdb=" CA LEU D 92 " pdb=" CB LEU D 92 " pdb=" CG LEU D 92 " ideal model delta sigma weight residual 116.30 127.02 -10.72 3.50e+00 8.16e-02 9.39e+00 angle pdb=" CA LEU B 92 " pdb=" CB LEU B 92 " pdb=" CG LEU B 92 " ideal model delta sigma weight residual 116.30 126.32 -10.02 3.50e+00 8.16e-02 8.20e+00 angle pdb=" C LYS B 203 " pdb=" CA LYS B 203 " pdb=" CB LYS B 203 " ideal model delta sigma weight residual 110.42 115.96 -5.54 1.99e+00 2.53e-01 7.75e+00 angle pdb=" CA GLN D 214 " pdb=" CB GLN D 214 " pdb=" CG GLN D 214 " ideal model delta sigma weight residual 114.10 118.88 -4.78 2.00e+00 2.50e-01 5.71e+00 ... (remaining 23371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9413 17.68 - 35.35: 783 35.35 - 53.03: 134 53.03 - 70.71: 7 70.71 - 88.39: 13 Dihedral angle restraints: 10350 sinusoidal: 4200 harmonic: 6150 Sorted by residual: dihedral pdb=" CA GLU F 89 " pdb=" C GLU F 89 " pdb=" N GLU F 90 " pdb=" CA GLU F 90 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU C 89 " pdb=" C GLU C 89 " pdb=" N GLU C 90 " pdb=" CA GLU C 90 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG E 23 " pdb=" C ARG E 23 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1868 0.045 - 0.090: 446 0.090 - 0.135: 282 0.135 - 0.180: 8 0.180 - 0.225: 6 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CB ILE D 185 " pdb=" CA ILE D 185 " pdb=" CG1 ILE D 185 " pdb=" CG2 ILE D 185 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE A 185 " pdb=" CA ILE A 185 " pdb=" CG1 ILE A 185 " pdb=" CG2 ILE A 185 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2607 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 276 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO F 277 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 277 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 277 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 276 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 277 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 277 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 277 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 276 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO C 277 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 277 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 277 " -0.024 5.00e-02 4.00e+02 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1050 2.73 - 3.27: 17097 3.27 - 3.82: 25599 3.82 - 4.36: 30721 4.36 - 4.90: 52817 Nonbonded interactions: 127284 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" O SER A 343 " model vdw 2.190 2.440 nonbonded pdb=" OG SER E 325 " pdb=" O SER E 343 " model vdw 2.191 2.440 nonbonded pdb=" OG SER C 325 " pdb=" O SER C 343 " model vdw 2.202 2.440 nonbonded pdb=" OG SER F 325 " pdb=" O SER F 343 " model vdw 2.207 2.440 nonbonded pdb=" OG SER B 325 " pdb=" O SER B 343 " model vdw 2.217 2.440 ... (remaining 127279 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 5.180 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 44.940 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17274 Z= 0.183 Angle : 0.599 10.882 23376 Z= 0.305 Chirality : 0.050 0.225 2610 Planarity : 0.005 0.053 3024 Dihedral : 13.107 88.387 6414 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.17), residues: 2148 helix: -0.70 (0.33), residues: 276 sheet: -0.97 (0.24), residues: 480 loop : -2.04 (0.15), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.144 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 outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2918 time to fit residues: 123.9399 Evaluate side-chains 219 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.0980 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 0.0980 chunk 87 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 17274 Z= 0.238 Angle : 0.611 9.927 23376 Z= 0.303 Chirality : 0.051 0.258 2610 Planarity : 0.005 0.042 3024 Dihedral : 4.661 19.354 2316 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2148 helix: -0.62 (0.33), residues: 276 sheet: -1.28 (0.23), residues: 486 loop : -2.06 (0.15), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.969 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 outliers start: 16 outliers final: 15 residues processed: 242 average time/residue: 0.2961 time to fit residues: 107.3132 Evaluate side-chains 237 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 222 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1509 time to fit residues: 7.0738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 196 optimal weight: 0.0570 chunk 212 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 overall best weight: 1.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 17274 Z= 0.209 Angle : 0.599 10.666 23376 Z= 0.290 Chirality : 0.050 0.299 2610 Planarity : 0.004 0.043 3024 Dihedral : 4.618 19.191 2316 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.17), residues: 2148 helix: -0.84 (0.32), residues: 270 sheet: -1.36 (0.23), residues: 486 loop : -2.07 (0.15), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 245 average time/residue: 0.2883 time to fit residues: 107.1363 Evaluate side-chains 222 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1468 time to fit residues: 3.1404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 131 optimal weight: 0.0070 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 17274 Z= 0.280 Angle : 0.623 11.043 23376 Z= 0.305 Chirality : 0.051 0.292 2610 Planarity : 0.005 0.055 3024 Dihedral : 4.761 19.602 2316 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.05 % Favored : 91.85 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.17), residues: 2148 helix: -0.50 (0.33), residues: 276 sheet: -1.47 (0.23), residues: 486 loop : -2.08 (0.15), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 224 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 229 average time/residue: 0.2857 time to fit residues: 100.9406 Evaluate side-chains 227 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1512 time to fit residues: 5.9136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 0.0010 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.0670 chunk 187 optimal weight: 6.9990 chunk 52 optimal weight: 0.0570 overall best weight: 0.6246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 17274 Z= 0.148 Angle : 0.584 11.616 23376 Z= 0.280 Chirality : 0.050 0.269 2610 Planarity : 0.004 0.043 3024 Dihedral : 4.507 19.002 2316 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.17), residues: 2148 helix: -0.43 (0.33), residues: 276 sheet: -1.40 (0.23), residues: 486 loop : -2.06 (0.15), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 227 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 233 average time/residue: 0.2865 time to fit residues: 103.2410 Evaluate side-chains 220 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 213 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1509 time to fit residues: 4.5916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 17274 Z= 0.501 Angle : 0.693 10.364 23376 Z= 0.349 Chirality : 0.053 0.251 2610 Planarity : 0.005 0.046 3024 Dihedral : 5.123 20.378 2316 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.43 % Favored : 89.39 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.17), residues: 2148 helix: -0.92 (0.29), residues: 306 sheet: -1.67 (0.22), residues: 546 loop : -2.17 (0.15), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 34 residues processed: 248 average time/residue: 0.2834 time to fit residues: 109.1013 Evaluate side-chains 248 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 2.136 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1559 time to fit residues: 13.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 118 optimal weight: 0.2980 chunk 175 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 17274 Z= 0.147 Angle : 0.598 11.972 23376 Z= 0.288 Chirality : 0.050 0.223 2610 Planarity : 0.004 0.044 3024 Dihedral : 4.674 19.333 2316 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.17), residues: 2148 helix: -1.05 (0.29), residues: 306 sheet: -1.45 (0.22), residues: 534 loop : -2.10 (0.16), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 223 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 230 average time/residue: 0.2714 time to fit residues: 97.1193 Evaluate side-chains 218 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1646 time to fit residues: 5.0456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 17274 Z= 0.474 Angle : 0.696 10.949 23376 Z= 0.350 Chirality : 0.054 0.410 2610 Planarity : 0.005 0.040 3024 Dihedral : 5.167 20.129 2316 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.17 % Favored : 88.55 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.17), residues: 2148 helix: -0.96 (0.29), residues: 306 sheet: -1.57 (0.21), residues: 570 loop : -2.27 (0.15), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 227 average time/residue: 0.2741 time to fit residues: 96.8960 Evaluate side-chains 223 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1648 time to fit residues: 6.0139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 175 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 17274 Z= 0.267 Angle : 0.632 11.524 23376 Z= 0.309 Chirality : 0.052 0.375 2610 Planarity : 0.004 0.040 3024 Dihedral : 4.986 19.748 2316 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.40 % Favored : 92.32 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.17), residues: 2148 helix: -0.89 (0.29), residues: 306 sheet: -1.63 (0.21), residues: 534 loop : -2.21 (0.15), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 216 average time/residue: 0.2654 time to fit residues: 90.3329 Evaluate side-chains 216 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1496 time to fit residues: 4.0337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 17274 Z= 0.327 Angle : 0.648 11.691 23376 Z= 0.319 Chirality : 0.052 0.370 2610 Planarity : 0.004 0.039 3024 Dihedral : 5.048 19.734 2316 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.57 % Favored : 89.15 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.17), residues: 2148 helix: -0.88 (0.29), residues: 306 sheet: -1.65 (0.21), residues: 534 loop : -2.26 (0.15), residues: 1308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 217 average time/residue: 0.2688 time to fit residues: 91.7622 Evaluate side-chains 218 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 213 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1488 time to fit residues: 4.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 171 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** 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 = 0.4203 r_free = 0.4203 target = 0.183958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108138 restraints weight = 21245.724| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.47 r_work: 0.3201 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 17274 Z= 0.156 Angle : 0.611 12.560 23376 Z= 0.293 Chirality : 0.050 0.347 2610 Planarity : 0.004 0.039 3024 Dihedral : 4.732 18.985 2316 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.17), residues: 2148 helix: -0.98 (0.29), residues: 306 sheet: -1.54 (0.22), residues: 534 loop : -2.19 (0.16), residues: 1308 =============================================================================== Job complete usr+sys time: 3443.14 seconds wall clock time: 63 minutes 14.85 seconds (3794.85 seconds total)