Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 15:55:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/04_2023/8d65_27217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/04_2023/8d65_27217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/04_2023/8d65_27217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/04_2023/8d65_27217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/04_2023/8d65_27217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/04_2023/8d65_27217_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 8365 2.51 5 N 2080 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 263": "OD1" <-> "OD2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 263": "OD1" <-> "OD2" Residue "E GLU 292": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12780 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.00, per 1000 atoms: 0.55 Number of scatterers: 12780 At special positions: 0 Unit cell: (91.3, 91.3, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 5 15.00 O 2300 8.00 N 2080 7.00 C 8365 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: 4.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 15 sheets defined 29.7% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.582A pdb=" N GLU A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 67 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 229 through 251 Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.715A pdb=" N ILE A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'B' and resid 60 through 67 removed outlier: 3.583A pdb=" N GLU B 64 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 229 through 251 Processing helix chain 'B' and resid 261 through 284 removed outlier: 3.716A pdb=" N ILE B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.582A pdb=" N GLU C 64 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 229 through 251 Processing helix chain 'C' and resid 261 through 285 removed outlier: 3.716A pdb=" N ILE C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'D' and resid 60 through 67 removed outlier: 3.583A pdb=" N GLU D 64 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE D 67 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 229 through 251 Processing helix chain 'D' and resid 261 through 284 removed outlier: 3.716A pdb=" N ILE D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'E' and resid 60 through 67 removed outlier: 3.582A pdb=" N GLU E 64 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE E 67 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 229 through 251 Processing helix chain 'E' and resid 261 through 284 removed outlier: 3.716A pdb=" N ILE E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 304 through 316 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 59 removed outlier: 6.868A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 40 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE A 18 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLN A 42 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL A 16 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N THR A 44 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL A 14 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 147 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 20 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= C, first strand: chain 'A' and resid 167 through 174 Processing sheet with id= D, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.867A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL B 40 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE B 18 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLN B 42 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL B 16 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR B 44 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL B 14 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 147 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE B 20 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= F, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= G, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.867A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL C 40 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 18 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLN C 42 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL C 16 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR C 44 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL C 14 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL C 147 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 20 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= I, first strand: chain 'C' and resid 167 through 174 Processing sheet with id= J, first strand: chain 'D' and resid 56 through 59 removed outlier: 6.868A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL D 40 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE D 18 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN D 42 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL D 16 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR D 44 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL D 14 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL D 147 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE D 20 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'D' and resid 167 through 174 Processing sheet with id= M, first strand: chain 'E' and resid 56 through 59 removed outlier: 6.867A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL E 40 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE E 18 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN E 42 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL E 16 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR E 44 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL E 14 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL E 147 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE E 20 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= O, first strand: chain 'E' and resid 167 through 174 531 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3250 1.33 - 1.45: 2673 1.45 - 1.57: 7132 1.57 - 1.69: 10 1.69 - 1.81: 50 Bond restraints: 13115 Sorted by residual: bond pdb=" C19 PGW D 401 " pdb=" O03 PGW D 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C1 PGW C 401 " pdb=" O01 PGW C 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C19 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C1 PGW D 401 " pdb=" O01 PGW D 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 13110 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 285 105.68 - 112.79: 6897 112.79 - 119.90: 4555 119.90 - 127.01: 5901 127.01 - 134.12: 177 Bond angle restraints: 17815 Sorted by residual: angle pdb=" N ILE A 152 " pdb=" CA ILE A 152 " pdb=" C ILE A 152 " ideal model delta sigma weight residual 108.12 117.33 -9.21 1.34e+00 5.57e-01 4.73e+01 angle pdb=" N ILE D 152 " pdb=" CA ILE D 152 " pdb=" C ILE D 152 " ideal model delta sigma weight residual 108.12 117.31 -9.19 1.34e+00 5.57e-01 4.70e+01 angle pdb=" N ILE E 152 " pdb=" CA ILE E 152 " pdb=" C ILE E 152 " ideal model delta sigma weight residual 108.12 117.30 -9.18 1.34e+00 5.57e-01 4.69e+01 angle pdb=" N ILE B 152 " pdb=" CA ILE B 152 " pdb=" C ILE B 152 " ideal model delta sigma weight residual 108.12 117.29 -9.17 1.34e+00 5.57e-01 4.68e+01 angle pdb=" N ILE C 152 " pdb=" CA ILE C 152 " pdb=" C ILE C 152 " ideal model delta sigma weight residual 108.12 117.28 -9.16 1.34e+00 5.57e-01 4.67e+01 ... (remaining 17810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 7250 24.04 - 48.08: 340 48.08 - 72.13: 80 72.13 - 96.17: 15 96.17 - 120.21: 10 Dihedral angle restraints: 7695 sinusoidal: 3190 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU C 118 " pdb=" C LEU C 118 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " ideal model delta harmonic sigma weight residual -180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual 180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 7692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1325 0.059 - 0.118: 481 0.118 - 0.177: 95 0.177 - 0.235: 38 0.235 - 0.294: 21 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA ASP A 153 " pdb=" N ASP A 153 " pdb=" C ASP A 153 " pdb=" CB ASP A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASP D 153 " pdb=" N ASP D 153 " pdb=" C ASP D 153 " pdb=" CB ASP D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASP B 153 " pdb=" N ASP B 153 " pdb=" C ASP B 153 " pdb=" CB ASP B 153 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1957 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 50 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO B 51 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 50 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO E 51 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 51 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 51 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 50 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 51 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " -0.028 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 38 2.48 - 3.08: 8307 3.08 - 3.69: 17557 3.69 - 4.29: 26300 4.29 - 4.90: 46783 Nonbonded interactions: 98985 Sorted by model distance: nonbonded pdb=" CZ PHE A 247 " pdb=" CE2 PHE B 247 " model vdw 1.871 3.640 nonbonded pdb=" CE1 PHE A 247 " pdb=" CE2 PHE B 247 " model vdw 1.965 3.640 nonbonded pdb=" CZ PHE D 247 " pdb=" CE2 PHE E 247 " model vdw 1.978 3.640 nonbonded pdb=" CE1 PHE D 247 " pdb=" CE2 PHE E 247 " model vdw 2.138 3.640 nonbonded pdb=" CE1 PHE B 247 " pdb=" CE2 PHE C 247 " model vdw 2.160 3.640 ... (remaining 98980 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 2.440 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 33.730 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.010 0.122 13115 Z= 0.612 Angle : 1.028 9.308 17815 Z= 0.610 Chirality : 0.069 0.294 1960 Planarity : 0.005 0.051 2250 Dihedral : 15.703 120.209 4785 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.19), residues: 1525 helix: -2.12 (0.18), residues: 530 sheet: -1.23 (0.24), residues: 505 loop : -2.83 (0.24), residues: 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2784 time to fit residues: 62.6592 Evaluate side-chains 96 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 103 ASN A 177 HIS A 184 ASN A 185 GLN A 264 GLN B 60 ASN B 177 HIS B 184 ASN B 185 GLN B 264 GLN C 60 ASN C 177 HIS C 184 ASN C 185 GLN D 60 ASN D 184 ASN D 185 GLN D 264 GLN E 60 ASN E 184 ASN E 185 GLN E 264 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13115 Z= 0.179 Angle : 0.489 5.383 17815 Z= 0.259 Chirality : 0.045 0.138 1960 Planarity : 0.004 0.036 2250 Dihedral : 10.554 70.820 1855 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.21), residues: 1525 helix: -0.37 (0.22), residues: 525 sheet: -0.73 (0.24), residues: 505 loop : -2.31 (0.24), residues: 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.485 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.1873 time to fit residues: 37.5778 Evaluate side-chains 109 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1206 time to fit residues: 4.5607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 13115 Z= 0.273 Angle : 0.499 5.109 17815 Z= 0.261 Chirality : 0.046 0.148 1960 Planarity : 0.004 0.034 2250 Dihedral : 9.247 75.875 1855 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1525 helix: 0.33 (0.23), residues: 535 sheet: -0.49 (0.25), residues: 505 loop : -2.10 (0.24), residues: 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.563 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 122 average time/residue: 0.1918 time to fit residues: 38.7454 Evaluate side-chains 107 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1209 time to fit residues: 4.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0770 chunk 102 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.7942 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13115 Z= 0.222 Angle : 0.466 5.021 17815 Z= 0.243 Chirality : 0.045 0.141 1960 Planarity : 0.003 0.032 2250 Dihedral : 8.799 79.977 1855 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1525 helix: 0.92 (0.24), residues: 525 sheet: -0.27 (0.25), residues: 505 loop : -2.09 (0.24), residues: 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.395 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.1853 time to fit residues: 33.0363 Evaluate side-chains 96 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1162 time to fit residues: 2.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 130 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13115 Z= 0.170 Angle : 0.435 4.999 17815 Z= 0.226 Chirality : 0.044 0.137 1960 Planarity : 0.003 0.029 2250 Dihedral : 8.441 81.575 1855 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1525 helix: 1.16 (0.24), residues: 535 sheet: -0.04 (0.25), residues: 505 loop : -1.89 (0.25), residues: 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.456 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 103 average time/residue: 0.1859 time to fit residues: 32.1372 Evaluate side-chains 89 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1500 time to fit residues: 2.1739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7933 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 13115 Z= 0.166 Angle : 0.432 4.957 17815 Z= 0.225 Chirality : 0.044 0.138 1960 Planarity : 0.003 0.028 2250 Dihedral : 8.317 82.869 1855 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1525 helix: 1.37 (0.24), residues: 535 sheet: 0.09 (0.25), residues: 505 loop : -1.84 (0.25), residues: 485 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.461 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 100 average time/residue: 0.1978 time to fit residues: 32.2767 Evaluate side-chains 91 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1202 time to fit residues: 2.3316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 66 optimal weight: 0.0470 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 0.0050 overall best weight: 1.8096 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 13115 Z= 0.226 Angle : 0.457 4.985 17815 Z= 0.238 Chirality : 0.046 0.143 1960 Planarity : 0.003 0.030 2250 Dihedral : 8.391 87.372 1855 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1525 helix: 1.41 (0.24), residues: 535 sheet: -0.18 (0.25), residues: 475 loop : -1.52 (0.25), residues: 515 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.474 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 107 average time/residue: 0.1927 time to fit residues: 34.0459 Evaluate side-chains 101 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1268 time to fit residues: 2.7483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7933 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 13115 Z= 0.158 Angle : 0.430 4.978 17815 Z= 0.224 Chirality : 0.044 0.137 1960 Planarity : 0.003 0.029 2250 Dihedral : 8.126 87.817 1855 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1525 helix: 1.56 (0.24), residues: 535 sheet: 0.01 (0.25), residues: 475 loop : -1.43 (0.25), residues: 515 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.299 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.1801 time to fit residues: 29.4149 Evaluate side-chains 89 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1111 time to fit residues: 2.4892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 0.1980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 13115 Z= 0.334 Angle : 0.510 5.654 17815 Z= 0.267 Chirality : 0.048 0.157 1960 Planarity : 0.004 0.031 2250 Dihedral : 8.412 86.547 1855 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1525 helix: 1.39 (0.24), residues: 535 sheet: 0.09 (0.25), residues: 505 loop : -1.90 (0.25), residues: 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.468 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.1999 time to fit residues: 34.6585 Evaluate side-chains 99 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1182 time to fit residues: 2.5701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 94 optimal weight: 0.0570 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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: 0.7928 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 13115 Z= 0.143 Angle : 0.434 4.892 17815 Z= 0.227 Chirality : 0.044 0.135 1960 Planarity : 0.003 0.029 2250 Dihedral : 7.913 85.849 1855 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1525 helix: 1.60 (0.24), residues: 535 sheet: 0.35 (0.25), residues: 505 loop : -1.76 (0.25), residues: 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.584 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.1898 time to fit residues: 30.8241 Evaluate side-chains 91 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1272 time to fit residues: 2.3687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 0.0870 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 6 optimal weight: 0.0170 chunk 86 optimal weight: 6.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107272 restraints weight = 14085.194| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.61 r_work: 0.2964 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 13115 Z= 0.160 Angle : 0.437 4.918 17815 Z= 0.228 Chirality : 0.045 0.139 1960 Planarity : 0.003 0.029 2250 Dihedral : 7.780 86.112 1855 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.07 % 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: 0.34 (0.23), residues: 1525 helix: 1.69 (0.24), residues: 535 sheet: 0.47 (0.25), residues: 505 loop : -1.73 (0.25), residues: 485 =============================================================================== Job complete usr+sys time: 2119.33 seconds wall clock time: 39 minutes 26.96 seconds (2366.96 seconds total)