Starting phenix.real_space_refine on Sat Feb 17 00:44:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/02_2024/7whr_32509.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/02_2024/7whr_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_32509/02_2024/7whr_32509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/02_2024/7whr_32509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/02_2024/7whr_32509.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whr_32509/02_2024/7whr_32509.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.33, per 1000 atoms: 0.55 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: 6.43 Conformation dependent library (CDL) restraints added in 3.1 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: 2.06 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: 5.35 Time building geometry restraints manager: 6.95 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.530 Check model and map are aligned: 0.230 Set scattering table: 0.180 Process input model: 45.710 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.700 ------------------------------------------------------------------------------- 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 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 224 HIS 0.002 0.001 HIS B 371 PHE 0.017 0.001 PHE E 218 TYR 0.008 0.001 TYR E 233 ARG 0.002 0.000 ARG B 77 *********************** 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 : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.8059 (ttp) cc_final: 0.7801 (ttm) REVERT: B 237 MET cc_start: 0.7643 (ttp) cc_final: 0.7378 (ttp) REVERT: A 102 ARG cc_start: 0.8188 (tmt170) cc_final: 0.7866 (tpt90) REVERT: A 370 GLU cc_start: 0.8120 (pm20) cc_final: 0.7380 (pm20) REVERT: C 72 MET cc_start: 0.8242 (ttp) cc_final: 0.8025 (ttm) REVERT: C 118 ASP cc_start: 0.8363 (m-30) cc_final: 0.7982 (m-30) REVERT: C 225 MET cc_start: 0.7702 (ptp) cc_final: 0.7475 (ptp) REVERT: D 72 MET cc_start: 0.8061 (ttp) cc_final: 0.7795 (ttm) REVERT: D 135 HIS cc_start: 0.7218 (m90) cc_final: 0.6766 (m90) REVERT: D 237 MET cc_start: 0.7636 (ttp) cc_final: 0.7373 (ttp) REVERT: E 102 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7913 (tpt90) REVERT: E 370 GLU cc_start: 0.8125 (pm20) cc_final: 0.7381 (pm20) REVERT: F 72 MET cc_start: 0.8228 (ttp) cc_final: 0.8002 (ttm) REVERT: F 118 ASP cc_start: 0.8347 (m-30) cc_final: 0.7933 (m-30) REVERT: F 225 MET cc_start: 0.7675 (ptp) cc_final: 0.7420 (ptp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2811 time to fit residues: 119.0520 Evaluate side-chains 223 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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: 0.4980 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 0.3980 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: 1.6784 ------------------------------------------------------------------------------- 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: 0.7165 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17274 Z= 0.254 Angle : 0.619 9.908 23376 Z= 0.307 Chirality : 0.051 0.267 2610 Planarity : 0.005 0.043 3024 Dihedral : 4.694 19.394 2316 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.98 % Allowed : 7.60 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.17), residues: 2148 helix: -0.93 (0.31), residues: 270 sheet: -1.30 (0.23), residues: 486 loop : -2.08 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 224 HIS 0.003 0.001 HIS C 246 PHE 0.011 0.001 PHE E 36 TYR 0.013 0.001 TYR B 233 ARG 0.003 0.000 ARG C 64 *********************** 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 258 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.8021 (ttp) cc_final: 0.7749 (ttm) REVERT: B 106 MET cc_start: 0.8457 (mpp) cc_final: 0.8173 (mpp) REVERT: A 102 ARG cc_start: 0.8152 (tmt170) cc_final: 0.7826 (tpt90) REVERT: A 370 GLU cc_start: 0.8102 (pm20) cc_final: 0.7480 (pm20) REVERT: C 72 MET cc_start: 0.8028 (ttp) cc_final: 0.7747 (ttm) REVERT: C 118 ASP cc_start: 0.8467 (m-30) cc_final: 0.8064 (m-30) REVERT: C 225 MET cc_start: 0.7752 (ptp) cc_final: 0.7486 (ptp) REVERT: D 72 MET cc_start: 0.8027 (ttp) cc_final: 0.7777 (ttm) REVERT: D 106 MET cc_start: 0.8460 (mpp) cc_final: 0.8181 (mpp) REVERT: D 135 HIS cc_start: 0.7174 (m90) cc_final: 0.6704 (m90) REVERT: E 102 ARG cc_start: 0.8106 (tmt170) cc_final: 0.7860 (tpt90) REVERT: E 370 GLU cc_start: 0.8102 (pm20) cc_final: 0.7480 (pm20) REVERT: F 118 ASP cc_start: 0.8459 (m-30) cc_final: 0.8021 (m-30) REVERT: F 190 ILE cc_start: 0.8760 (tp) cc_final: 0.8482 (tt) REVERT: F 225 MET cc_start: 0.7759 (ptp) cc_final: 0.7480 (ptp) outliers start: 18 outliers final: 15 residues processed: 248 average time/residue: 0.3064 time to fit residues: 113.3196 Evaluate side-chains 239 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 224 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.2980 chunk 60 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 54 optimal weight: 0.0470 chunk 196 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 175 optimal weight: 0.1980 chunk 194 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 overall best weight: 1.2680 ------------------------------------------------------------------------------- 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: 0.7153 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17274 Z= 0.204 Angle : 0.597 10.822 23376 Z= 0.290 Chirality : 0.050 0.300 2610 Planarity : 0.004 0.051 3024 Dihedral : 4.615 19.265 2316 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.31 % Allowed : 12.57 % Favored : 86.12 % 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: -2.55 (0.17), residues: 2148 helix: -0.88 (0.32), residues: 270 sheet: -1.37 (0.23), residues: 486 loop : -2.08 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 224 HIS 0.003 0.001 HIS B 338 PHE 0.012 0.001 PHE E 218 TYR 0.013 0.001 TYR B 233 ARG 0.010 0.000 ARG E 77 *********************** 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 255 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 2.229 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: B 72 MET cc_start: 0.7966 (ttp) cc_final: 0.7612 (ttm) REVERT: B 190 ILE cc_start: 0.8713 (tp) cc_final: 0.8445 (tt) REVERT: A 102 ARG cc_start: 0.8142 (tmt170) cc_final: 0.7820 (tpt90) REVERT: A 281 ILE cc_start: 0.8694 (mm) cc_final: 0.8433 (tp) REVERT: A 370 GLU cc_start: 0.8104 (pm20) cc_final: 0.7478 (pm20) REVERT: C 72 MET cc_start: 0.8058 (ttp) cc_final: 0.7656 (ttm) REVERT: C 118 ASP cc_start: 0.8456 (m-30) cc_final: 0.8043 (m-30) REVERT: D 72 MET cc_start: 0.7956 (ttp) cc_final: 0.7597 (ttm) REVERT: D 135 HIS cc_start: 0.7169 (m90) cc_final: 0.6696 (m90) REVERT: D 209 MET cc_start: 0.7852 (tpt) cc_final: 0.7391 (tpt) REVERT: E 102 ARG cc_start: 0.8111 (tmt170) cc_final: 0.7855 (tpt90) REVERT: E 281 ILE cc_start: 0.8697 (mm) cc_final: 0.8440 (tp) REVERT: E 370 GLU cc_start: 0.8125 (pm20) cc_final: 0.7502 (pm20) REVERT: F 118 ASP cc_start: 0.8440 (m-30) cc_final: 0.7992 (m-30) REVERT: F 190 ILE cc_start: 0.8844 (tp) cc_final: 0.8512 (tt) outliers start: 24 outliers final: 15 residues processed: 245 average time/residue: 0.2955 time to fit residues: 109.0656 Evaluate side-chains 238 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS 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: 0.9990 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 0.0470 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.0370 chunk 56 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.7127 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17274 Z= 0.148 Angle : 0.586 11.525 23376 Z= 0.282 Chirality : 0.049 0.292 2610 Planarity : 0.004 0.060 3024 Dihedral : 4.474 19.025 2316 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.77 % Allowed : 15.74 % Favored : 83.50 % 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 (0.31), residues: 270 sheet: -1.35 (0.23), residues: 486 loop : -2.07 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 224 HIS 0.002 0.001 HIS D 338 PHE 0.008 0.001 PHE E 206 TYR 0.012 0.001 TYR B 233 ARG 0.012 0.000 ARG D 77 *********************** 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 244 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 230 time to evaluate : 1.939 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: B 72 MET cc_start: 0.7944 (ttp) cc_final: 0.7567 (ttm) REVERT: B 106 MET cc_start: 0.8275 (mpp) cc_final: 0.8059 (mpp) REVERT: B 190 ILE cc_start: 0.8742 (tp) cc_final: 0.8449 (tt) REVERT: A 102 ARG cc_start: 0.8138 (tmt170) cc_final: 0.7846 (tpt90) REVERT: A 281 ILE cc_start: 0.8677 (mm) cc_final: 0.8411 (tp) REVERT: A 370 GLU cc_start: 0.8123 (pm20) cc_final: 0.7487 (pm20) REVERT: C 72 MET cc_start: 0.8014 (ttp) cc_final: 0.7610 (ttm) REVERT: C 118 ASP cc_start: 0.8367 (m-30) cc_final: 0.7969 (m-30) REVERT: C 374 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 72 MET cc_start: 0.7984 (ttp) cc_final: 0.7634 (ttm) REVERT: D 106 MET cc_start: 0.8279 (mpp) cc_final: 0.8065 (mpp) REVERT: D 135 HIS cc_start: 0.7099 (m90) cc_final: 0.6658 (m90) REVERT: D 190 ILE cc_start: 0.8764 (tp) cc_final: 0.8474 (tt) REVERT: E 102 ARG cc_start: 0.8112 (tmt170) cc_final: 0.7853 (tpt90) REVERT: E 281 ILE cc_start: 0.8680 (mm) cc_final: 0.8418 (tp) REVERT: E 370 GLU cc_start: 0.8122 (pm20) cc_final: 0.7488 (pm20) REVERT: F 118 ASP cc_start: 0.8363 (m-30) cc_final: 0.7964 (m-30) REVERT: F 190 ILE cc_start: 0.8850 (tp) cc_final: 0.8647 (tp) outliers start: 14 outliers final: 13 residues processed: 233 average time/residue: 0.2985 time to fit residues: 105.2022 Evaluate side-chains 237 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 187 optimal weight: 0.2980 chunk 52 optimal weight: 0.1980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7182 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17274 Z= 0.274 Angle : 0.602 10.777 23376 Z= 0.295 Chirality : 0.050 0.269 2610 Planarity : 0.004 0.043 3024 Dihedral : 4.655 19.468 2316 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.50 % Favored : 92.36 % Rotamer: Outliers : 1.42 % Allowed : 17.76 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.17), residues: 2148 helix: -0.33 (0.34), residues: 276 sheet: -1.48 (0.23), residues: 486 loop : -2.06 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 224 HIS 0.004 0.001 HIS B 338 PHE 0.010 0.001 PHE A 36 TYR 0.014 0.001 TYR B 233 ARG 0.006 0.000 ARG B 77 *********************** 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 251 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.7981 (ttp) cc_final: 0.7604 (ttm) REVERT: B 190 ILE cc_start: 0.8795 (tp) cc_final: 0.8430 (tt) REVERT: A 102 ARG cc_start: 0.8174 (tmt170) cc_final: 0.7852 (tpt90) REVERT: A 281 ILE cc_start: 0.8682 (mm) cc_final: 0.8437 (tp) REVERT: A 370 GLU cc_start: 0.8114 (pm20) cc_final: 0.7488 (pm20) REVERT: C 72 MET cc_start: 0.8020 (ttp) cc_final: 0.7661 (ttm) REVERT: C 118 ASP cc_start: 0.8502 (m-30) cc_final: 0.8138 (m-30) REVERT: C 374 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8395 (mm-30) REVERT: D 72 MET cc_start: 0.7992 (ttp) cc_final: 0.7630 (ttm) REVERT: D 190 ILE cc_start: 0.8721 (tp) cc_final: 0.8395 (tt) REVERT: E 102 ARG cc_start: 0.8100 (tmt170) cc_final: 0.7815 (tpt90) REVERT: E 281 ILE cc_start: 0.8682 (mm) cc_final: 0.8443 (tp) REVERT: E 370 GLU cc_start: 0.8137 (pm20) cc_final: 0.7512 (pm20) REVERT: F 118 ASP cc_start: 0.8491 (m-30) cc_final: 0.8090 (m-30) REVERT: F 190 ILE cc_start: 0.8938 (tp) cc_final: 0.8736 (tp) outliers start: 26 outliers final: 24 residues processed: 235 average time/residue: 0.2824 time to fit residues: 101.0724 Evaluate side-chains 245 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 221 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 246 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.0970 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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: 0.7181 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17274 Z= 0.255 Angle : 0.595 11.082 23376 Z= 0.290 Chirality : 0.050 0.247 2610 Planarity : 0.004 0.043 3024 Dihedral : 4.660 19.594 2316 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.12 % Favored : 92.69 % Rotamer: Outliers : 2.51 % Allowed : 17.76 % Favored : 79.73 % 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: -2.46 (0.17), residues: 2148 helix: -0.59 (0.31), residues: 312 sheet: -1.52 (0.23), residues: 486 loop : -2.01 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 224 HIS 0.004 0.001 HIS B 338 PHE 0.009 0.001 PHE E 36 TYR 0.013 0.001 TYR B 233 ARG 0.006 0.000 ARG D 77 *********************** 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 275 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 229 time to evaluate : 1.905 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: B 72 MET cc_start: 0.7981 (ttp) cc_final: 0.7554 (ttp) REVERT: A 102 ARG cc_start: 0.8181 (tmt170) cc_final: 0.7845 (tpt90) REVERT: A 281 ILE cc_start: 0.8776 (mm) cc_final: 0.8570 (tp) REVERT: A 370 GLU cc_start: 0.8147 (pm20) cc_final: 0.7528 (pm20) REVERT: C 72 MET cc_start: 0.8015 (ttp) cc_final: 0.7699 (ttm) REVERT: C 92 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6658 (mp) REVERT: C 118 ASP cc_start: 0.8530 (m-30) cc_final: 0.8128 (m-30) REVERT: C 374 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8398 (mm-30) REVERT: D 72 MET cc_start: 0.7977 (ttp) cc_final: 0.7537 (ttp) REVERT: D 190 ILE cc_start: 0.8732 (tp) cc_final: 0.8393 (tt) REVERT: E 102 ARG cc_start: 0.8109 (tmt170) cc_final: 0.7821 (tpt90) REVERT: E 281 ILE cc_start: 0.8774 (mm) cc_final: 0.8574 (tp) REVERT: E 370 GLU cc_start: 0.8146 (pm20) cc_final: 0.7529 (pm20) REVERT: F 118 ASP cc_start: 0.8519 (m-30) cc_final: 0.8113 (m-30) outliers start: 46 outliers final: 34 residues processed: 257 average time/residue: 0.2595 time to fit residues: 103.1899 Evaluate side-chains 252 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 246 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17274 Z= 0.151 Angle : 0.573 12.126 23376 Z= 0.275 Chirality : 0.050 0.380 2610 Planarity : 0.004 0.042 3024 Dihedral : 4.436 19.037 2316 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.28 % Favored : 93.67 % Rotamer: Outliers : 2.02 % Allowed : 18.42 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.17), residues: 2148 helix: -0.64 (0.32), residues: 270 sheet: -1.29 (0.23), residues: 474 loop : -2.09 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 224 HIS 0.002 0.001 HIS B 338 PHE 0.010 0.001 PHE E 206 TYR 0.011 0.001 TYR D 233 ARG 0.002 0.000 ARG B 77 *********************** 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 260 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 223 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.7931 (ttp) cc_final: 0.7530 (ttp) REVERT: A 102 ARG cc_start: 0.8134 (tmt170) cc_final: 0.7816 (tpt90) REVERT: A 281 ILE cc_start: 0.8776 (mm) cc_final: 0.8555 (tp) REVERT: A 370 GLU cc_start: 0.8134 (pm20) cc_final: 0.7503 (pm20) REVERT: C 72 MET cc_start: 0.7876 (ttp) cc_final: 0.7601 (ttm) REVERT: C 92 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6641 (mp) REVERT: C 118 ASP cc_start: 0.8499 (m-30) cc_final: 0.8077 (m-30) REVERT: C 281 ILE cc_start: 0.8677 (mm) cc_final: 0.8322 (tp) REVERT: C 374 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8264 (mm-30) REVERT: D 72 MET cc_start: 0.7927 (ttp) cc_final: 0.7503 (ttp) REVERT: D 190 ILE cc_start: 0.8801 (tp) cc_final: 0.8437 (tt) REVERT: E 102 ARG cc_start: 0.8080 (tmt170) cc_final: 0.7774 (tpt90) REVERT: E 281 ILE cc_start: 0.8773 (mm) cc_final: 0.8558 (tp) REVERT: E 370 GLU cc_start: 0.8132 (pm20) cc_final: 0.7503 (pm20) REVERT: F 118 ASP cc_start: 0.8441 (m-30) cc_final: 0.8017 (m-30) REVERT: F 190 ILE cc_start: 0.8711 (tp) cc_final: 0.8481 (tt) REVERT: F 281 ILE cc_start: 0.8677 (mm) cc_final: 0.8325 (tp) outliers start: 37 outliers final: 31 residues processed: 244 average time/residue: 0.2713 time to fit residues: 101.9507 Evaluate side-chains 242 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 246 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Chi-restraints excluded: chain F residue 320 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.0030 chunk 62 optimal weight: 0.0010 chunk 40 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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: 0.7160 moved from start: 0.1557 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= 0.210 Angle : 0.583 12.027 23376 Z= 0.282 Chirality : 0.050 0.331 2610 Planarity : 0.004 0.040 3024 Dihedral : 4.475 19.209 2316 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 2.08 % Allowed : 18.58 % Favored : 79.34 % 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: -0.78 (0.30), residues: 306 sheet: -1.29 (0.23), residues: 474 loop : -2.04 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 224 HIS 0.003 0.001 HIS B 338 PHE 0.010 0.001 PHE E 206 TYR 0.013 0.001 TYR D 233 ARG 0.003 0.000 ARG B 77 *********************** 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 249 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 211 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.7968 (ttp) cc_final: 0.7529 (ttp) REVERT: A 102 ARG cc_start: 0.8154 (tmt170) cc_final: 0.7823 (tpt90) REVERT: A 281 ILE cc_start: 0.8799 (mm) cc_final: 0.8578 (tp) REVERT: A 370 GLU cc_start: 0.8139 (pm20) cc_final: 0.7503 (pm20) REVERT: C 72 MET cc_start: 0.7858 (ttp) cc_final: 0.7568 (ttm) REVERT: C 92 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6611 (mp) REVERT: C 118 ASP cc_start: 0.8498 (m-30) cc_final: 0.8092 (m-30) REVERT: C 281 ILE cc_start: 0.8705 (mm) cc_final: 0.8480 (tp) REVERT: C 374 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 72 MET cc_start: 0.7981 (ttp) cc_final: 0.7561 (ttp) REVERT: D 190 ILE cc_start: 0.8818 (tp) cc_final: 0.8457 (tt) REVERT: E 102 ARG cc_start: 0.8130 (tmt170) cc_final: 0.7778 (tpt90) REVERT: E 281 ILE cc_start: 0.8799 (mm) cc_final: 0.8582 (tp) REVERT: E 370 GLU cc_start: 0.8137 (pm20) cc_final: 0.7504 (pm20) REVERT: F 118 ASP cc_start: 0.8484 (m-30) cc_final: 0.8072 (m-30) REVERT: F 190 ILE cc_start: 0.8716 (tp) cc_final: 0.8464 (tt) REVERT: F 281 ILE cc_start: 0.8707 (mm) cc_final: 0.8484 (tp) outliers start: 38 outliers final: 30 residues processed: 232 average time/residue: 0.2699 time to fit residues: 96.9337 Evaluate side-chains 240 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 246 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 0.0870 chunk 193 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- 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: 0.7167 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17274 Z= 0.223 Angle : 0.590 12.083 23376 Z= 0.286 Chirality : 0.050 0.320 2610 Planarity : 0.004 0.039 3024 Dihedral : 4.513 19.263 2316 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 1.97 % Allowed : 18.96 % Favored : 79.07 % 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: -0.76 (0.30), residues: 306 sheet: -1.31 (0.23), residues: 474 loop : -2.04 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 224 HIS 0.003 0.001 HIS D 338 PHE 0.009 0.001 PHE E 206 TYR 0.012 0.001 TYR D 233 ARG 0.003 0.000 ARG D 64 *********************** 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 244 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.7983 (ttp) cc_final: 0.7559 (ttp) REVERT: A 102 ARG cc_start: 0.8187 (tmt170) cc_final: 0.7826 (tpt90) REVERT: A 281 ILE cc_start: 0.8812 (mm) cc_final: 0.8599 (tp) REVERT: A 370 GLU cc_start: 0.8135 (pm20) cc_final: 0.7505 (pm20) REVERT: C 72 MET cc_start: 0.7897 (ttp) cc_final: 0.7608 (ttm) REVERT: C 92 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6580 (mp) REVERT: C 118 ASP cc_start: 0.8507 (m-30) cc_final: 0.8106 (m-30) REVERT: C 281 ILE cc_start: 0.8714 (mm) cc_final: 0.8494 (tp) REVERT: C 374 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8380 (mm-30) REVERT: D 72 MET cc_start: 0.7978 (ttp) cc_final: 0.7563 (ttp) REVERT: D 190 ILE cc_start: 0.8817 (tp) cc_final: 0.8473 (tt) REVERT: E 102 ARG cc_start: 0.8092 (tmt170) cc_final: 0.7746 (tpt90) REVERT: E 281 ILE cc_start: 0.8811 (mm) cc_final: 0.8603 (tp) REVERT: E 370 GLU cc_start: 0.8136 (pm20) cc_final: 0.7506 (pm20) REVERT: F 118 ASP cc_start: 0.8496 (m-30) cc_final: 0.8087 (m-30) REVERT: F 190 ILE cc_start: 0.8736 (tp) cc_final: 0.8483 (tt) REVERT: F 281 ILE cc_start: 0.8716 (mm) cc_final: 0.8497 (tp) outliers start: 36 outliers final: 28 residues processed: 230 average time/residue: 0.2622 time to fit residues: 93.5885 Evaluate side-chains 236 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17274 Z= 0.215 Angle : 0.591 12.305 23376 Z= 0.288 Chirality : 0.050 0.314 2610 Planarity : 0.004 0.039 3024 Dihedral : 4.517 19.249 2316 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 1.64 % Allowed : 19.23 % Favored : 79.13 % 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: -0.73 (0.30), residues: 306 sheet: -1.35 (0.23), residues: 474 loop : -2.03 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 PHE 0.009 0.001 PHE E 206 TYR 0.012 0.001 TYR D 233 ARG 0.004 0.000 ARG B 77 ********************** 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 239 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.7994 (ttp) cc_final: 0.7595 (ttp) REVERT: A 102 ARG cc_start: 0.8192 (tmt170) cc_final: 0.7825 (tpt90) REVERT: A 370 GLU cc_start: 0.8154 (pm20) cc_final: 0.7534 (pm20) REVERT: C 72 MET cc_start: 0.7910 (ttp) cc_final: 0.7613 (ttm) REVERT: C 92 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6537 (mp) REVERT: C 118 ASP cc_start: 0.8501 (m-30) cc_final: 0.8100 (m-30) REVERT: C 281 ILE cc_start: 0.8724 (mm) cc_final: 0.8371 (tp) REVERT: C 374 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8352 (mm-30) REVERT: D 72 MET cc_start: 0.7974 (ttp) cc_final: 0.7608 (ttm) REVERT: D 107 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8652 (tm-30) REVERT: D 190 ILE cc_start: 0.8818 (tp) cc_final: 0.8483 (tt) REVERT: E 102 ARG cc_start: 0.8104 (tmt170) cc_final: 0.7783 (tpt90) REVERT: E 370 GLU cc_start: 0.8144 (pm20) cc_final: 0.7523 (pm20) REVERT: F 118 ASP cc_start: 0.8491 (m-30) cc_final: 0.8081 (m-30) REVERT: F 190 ILE cc_start: 0.8740 (tp) cc_final: 0.8486 (tt) REVERT: F 281 ILE cc_start: 0.8718 (mm) cc_final: 0.8364 (tp) outliers start: 30 outliers final: 28 residues processed: 227 average time/residue: 0.2546 time to fit residues: 90.1104 Evaluate side-chains 237 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.183882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108301 restraints weight = 21294.321| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.49 r_work: 0.3200 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17274 Z= 0.185 Angle : 0.590 12.419 23376 Z= 0.285 Chirality : 0.050 0.310 2610 Planarity : 0.004 0.038 3024 Dihedral : 4.469 19.092 2316 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 1.69 % Allowed : 19.62 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.17), residues: 2148 helix: -0.73 (0.30), residues: 306 sheet: -1.30 (0.23), residues: 474 loop : -2.03 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 224 HIS 0.002 0.001 HIS D 338 PHE 0.008 0.001 PHE E 206 TYR 0.012 0.001 TYR D 233 ARG 0.008 0.000 ARG A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3482.10 seconds wall clock time: 63 minutes 59.66 seconds (3839.66 seconds total)