Starting phenix.real_space_refine on Fri Mar 15 21:13:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/03_2024/8d65_27217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/03_2024/8d65_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_27217/03_2024/8d65_27217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/03_2024/8d65_27217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/03_2024/8d65_27217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d65_27217/03_2024/8d65_27217_updated.pdb" } resolution = 3.47 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= 0.009 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-dev-5265/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: 7.02, 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: 4.80 Conformation dependent library (CDL) restraints added in 2.1 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: 2.38 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: 3.58 Time building geometry restraints manager: 5.21 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: 7290 24.04 - 48.08: 365 48.08 - 72.13: 80 72.13 - 96.17: 15 96.17 - 120.21: 10 Dihedral angle restraints: 7760 sinusoidal: 3255 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 7757 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: 0.310 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: 1.970 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.050 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- 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 : 15.837 120.209 4850 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 % Allowed : 7.49 % Favored : 92.51 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 206 HIS 0.004 0.001 HIS C 284 PHE 0.017 0.003 PHE E 304 TYR 0.009 0.002 TYR B 245 ARG 0.003 0.000 ARG A 117 *********************** 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 : 1.359 Fit side-chains REVERT: A 90 LYS cc_start: 0.9061 (pttt) cc_final: 0.8545 (pttm) REVERT: A 149 THR cc_start: 0.8989 (p) cc_final: 0.8700 (t) REVERT: A 245 TYR cc_start: 0.8935 (t80) cc_final: 0.8203 (t80) REVERT: B 226 GLU cc_start: 0.7405 (mp0) cc_final: 0.6989 (mp0) REVERT: B 252 ILE cc_start: 0.8248 (mm) cc_final: 0.7960 (mm) REVERT: C 38 TYR cc_start: 0.8547 (m-80) cc_final: 0.8332 (m-80) REVERT: C 90 LYS cc_start: 0.9102 (pttt) cc_final: 0.8649 (pttm) REVERT: C 149 THR cc_start: 0.8972 (p) cc_final: 0.8768 (t) REVERT: C 191 ILE cc_start: 0.9100 (mt) cc_final: 0.8889 (mt) REVERT: D 149 THR cc_start: 0.9149 (p) cc_final: 0.8807 (t) REVERT: D 226 GLU cc_start: 0.7654 (mp0) cc_final: 0.7223 (mp0) REVERT: E 86 ASP cc_start: 0.7824 (m-30) cc_final: 0.7492 (m-30) REVERT: E 149 THR cc_start: 0.9099 (p) cc_final: 0.8730 (t) REVERT: E 191 ILE cc_start: 0.9130 (mt) cc_final: 0.8857 (mt) REVERT: E 245 TYR cc_start: 0.8702 (t80) cc_final: 0.8402 (t80) REVERT: E 252 ILE cc_start: 0.8326 (mm) cc_final: 0.8109 (mm) REVERT: E 282 PHE cc_start: 0.8047 (t80) cc_final: 0.7837 (t80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2745 time to fit residues: 62.0057 Evaluate side-chains 102 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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: 0.6980 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: 10.0000 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13115 Z= 0.174 Angle : 0.484 5.401 17815 Z= 0.255 Chirality : 0.045 0.137 1960 Planarity : 0.004 0.036 2250 Dihedral : 11.676 76.157 1920 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.24 % Allowed : 9.89 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.21), residues: 1525 helix: -0.34 (0.22), residues: 525 sheet: -0.71 (0.24), residues: 505 loop : -2.32 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 206 HIS 0.001 0.000 HIS B 284 PHE 0.033 0.001 PHE E 247 TYR 0.011 0.001 TYR B 248 ARG 0.005 0.000 ARG A 255 *********************** 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: 17 poor density : 108 time to evaluate : 1.341 Fit side-chains REVERT: A 90 LYS cc_start: 0.9093 (pttt) cc_final: 0.8582 (pttm) REVERT: A 149 THR cc_start: 0.9005 (p) cc_final: 0.8771 (t) REVERT: A 245 TYR cc_start: 0.8776 (t80) cc_final: 0.7868 (t80) REVERT: B 114 MET cc_start: 0.9094 (mtt) cc_final: 0.8872 (mtt) REVERT: B 226 GLU cc_start: 0.7359 (mp0) cc_final: 0.7037 (mp0) REVERT: C 90 LYS cc_start: 0.9058 (pttt) cc_final: 0.8606 (pttm) REVERT: D 245 TYR cc_start: 0.8606 (t80) cc_final: 0.7978 (t80) REVERT: E 86 ASP cc_start: 0.7784 (m-30) cc_final: 0.7506 (m-30) REVERT: E 282 PHE cc_start: 0.8040 (t80) cc_final: 0.7803 (t80) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 0.1967 time to fit residues: 38.9071 Evaluate side-chains 109 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 186 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 0.0980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN C 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13115 Z= 0.259 Angle : 0.491 5.069 17815 Z= 0.257 Chirality : 0.046 0.146 1960 Planarity : 0.004 0.032 2250 Dihedral : 10.530 82.297 1920 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.82 % Allowed : 10.69 % Favored : 87.49 % 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: -1.13 (0.22), residues: 1525 helix: 0.29 (0.23), residues: 535 sheet: -0.46 (0.25), residues: 505 loop : -2.12 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 220 HIS 0.002 0.001 HIS E 284 PHE 0.033 0.002 PHE E 247 TYR 0.009 0.001 TYR E 245 ARG 0.003 0.000 ARG B 255 *********************** 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 132 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.440 Fit side-chains REVERT: A 90 LYS cc_start: 0.9112 (pttt) cc_final: 0.8591 (pttm) REVERT: A 245 TYR cc_start: 0.8813 (t80) cc_final: 0.7891 (t80) REVERT: B 226 GLU cc_start: 0.7433 (mp0) cc_final: 0.7094 (mp0) REVERT: D 94 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8278 (mt) REVERT: D 245 TYR cc_start: 0.8628 (t80) cc_final: 0.7910 (t80) REVERT: E 86 ASP cc_start: 0.7757 (m-30) cc_final: 0.7420 (m-30) REVERT: E 282 PHE cc_start: 0.8025 (t80) cc_final: 0.7821 (t80) outliers start: 25 outliers final: 18 residues processed: 129 average time/residue: 0.1811 time to fit residues: 38.4276 Evaluate side-chains 121 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 186 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13115 Z= 0.238 Angle : 0.473 5.012 17815 Z= 0.246 Chirality : 0.046 0.143 1960 Planarity : 0.003 0.030 2250 Dihedral : 10.207 85.532 1920 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.18 % Allowed : 11.49 % Favored : 86.33 % 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: -0.77 (0.22), residues: 1525 helix: 0.71 (0.23), residues: 535 sheet: -0.31 (0.25), residues: 505 loop : -2.02 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 220 HIS 0.002 0.001 HIS C 284 PHE 0.030 0.001 PHE E 247 TYR 0.007 0.001 TYR E 245 ARG 0.002 0.000 ARG C 255 *********************** 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 142 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.490 Fit side-chains REVERT: A 90 LYS cc_start: 0.9085 (pttt) cc_final: 0.8555 (pttm) REVERT: A 105 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8205 (ttt180) REVERT: B 226 GLU cc_start: 0.7429 (mp0) cc_final: 0.7111 (mp0) REVERT: D 94 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8288 (mt) REVERT: D 245 TYR cc_start: 0.8620 (t80) cc_final: 0.7946 (t80) REVERT: E 86 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: E 282 PHE cc_start: 0.8053 (t80) cc_final: 0.7844 (t80) outliers start: 30 outliers final: 22 residues processed: 138 average time/residue: 0.1848 time to fit residues: 41.4875 Evaluate side-chains 127 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 186 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 0.0970 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13115 Z= 0.240 Angle : 0.469 5.022 17815 Z= 0.244 Chirality : 0.046 0.145 1960 Planarity : 0.003 0.029 2250 Dihedral : 10.055 88.753 1920 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.11 % Allowed : 12.44 % Favored : 85.45 % 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: -0.55 (0.22), residues: 1525 helix: 0.96 (0.23), residues: 535 sheet: -0.20 (0.25), residues: 505 loop : -1.99 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.002 0.001 HIS B 284 PHE 0.032 0.002 PHE D 247 TYR 0.007 0.001 TYR A 248 ARG 0.002 0.000 ARG C 255 *********************** 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 140 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.461 Fit side-chains REVERT: A 90 LYS cc_start: 0.9087 (pttt) cc_final: 0.8562 (pttm) REVERT: A 105 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8192 (ttt180) REVERT: B 226 GLU cc_start: 0.7475 (mp0) cc_final: 0.7152 (mp0) REVERT: B 245 TYR cc_start: 0.8666 (t80) cc_final: 0.8466 (t80) REVERT: B 256 LEU cc_start: 0.8665 (mt) cc_final: 0.8425 (mt) REVERT: C 270 TYR cc_start: 0.8002 (m-80) cc_final: 0.7652 (m-80) REVERT: D 94 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8305 (mt) REVERT: D 245 TYR cc_start: 0.8577 (t80) cc_final: 0.7898 (t80) REVERT: E 86 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: E 282 PHE cc_start: 0.8057 (t80) cc_final: 0.7800 (t80) outliers start: 29 outliers final: 23 residues processed: 137 average time/residue: 0.1870 time to fit residues: 41.7025 Evaluate side-chains 130 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 253 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13115 Z= 0.138 Angle : 0.427 4.893 17815 Z= 0.223 Chirality : 0.044 0.135 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.687 88.091 1920 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.89 % Allowed : 13.16 % Favored : 84.95 % 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: -0.18 (0.22), residues: 1525 helix: 1.31 (0.24), residues: 535 sheet: 0.04 (0.25), residues: 500 loop : -1.87 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 220 HIS 0.001 0.000 HIS E 284 PHE 0.022 0.001 PHE D 247 TYR 0.007 0.001 TYR E 245 ARG 0.001 0.000 ARG A 105 *********************** 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 130 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.409 Fit side-chains REVERT: A 90 LYS cc_start: 0.9061 (pttt) cc_final: 0.8539 (pttm) REVERT: A 105 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8107 (ttt180) REVERT: B 226 GLU cc_start: 0.7538 (mp0) cc_final: 0.7164 (mp0) REVERT: C 151 ASN cc_start: 0.6942 (m110) cc_final: 0.6740 (m110) REVERT: D 94 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8303 (mt) REVERT: D 245 TYR cc_start: 0.8508 (t80) cc_final: 0.7868 (t80) REVERT: E 86 ASP cc_start: 0.7790 (m-30) cc_final: 0.7548 (m-30) REVERT: E 282 PHE cc_start: 0.8037 (t80) cc_final: 0.7818 (t80) outliers start: 26 outliers final: 18 residues processed: 127 average time/residue: 0.2042 time to fit residues: 41.4276 Evaluate side-chains 113 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 144 optimal weight: 0.0170 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13115 Z= 0.264 Angle : 0.476 5.006 17815 Z= 0.247 Chirality : 0.046 0.143 1960 Planarity : 0.003 0.030 2250 Dihedral : 9.827 88.569 1920 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.82 % Allowed : 13.67 % Favored : 84.51 % 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: -0.20 (0.22), residues: 1525 helix: 1.34 (0.24), residues: 535 sheet: -0.01 (0.25), residues: 505 loop : -1.90 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 220 HIS 0.003 0.001 HIS B 284 PHE 0.022 0.002 PHE C 282 TYR 0.006 0.001 TYR A 248 ARG 0.002 0.000 ARG C 255 *********************** 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 133 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.483 Fit side-chains REVERT: A 90 LYS cc_start: 0.9091 (pttt) cc_final: 0.8556 (pttm) REVERT: A 105 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8194 (ttt180) REVERT: B 226 GLU cc_start: 0.7549 (mp0) cc_final: 0.7208 (mp0) REVERT: C 270 TYR cc_start: 0.7994 (m-80) cc_final: 0.7700 (m-80) REVERT: D 94 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8306 (mt) REVERT: D 245 TYR cc_start: 0.8596 (t80) cc_final: 0.7963 (t80) REVERT: E 86 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: E 282 PHE cc_start: 0.8047 (t80) cc_final: 0.7789 (t80) outliers start: 25 outliers final: 20 residues processed: 130 average time/residue: 0.1857 time to fit residues: 38.9394 Evaluate side-chains 125 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 253 LEU 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: 0.9980 chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13115 Z= 0.153 Angle : 0.433 4.877 17815 Z= 0.226 Chirality : 0.044 0.138 1960 Planarity : 0.003 0.029 2250 Dihedral : 9.610 88.644 1920 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.45 % Allowed : 14.33 % Favored : 84.22 % 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: 0.07 (0.23), residues: 1525 helix: 1.53 (0.24), residues: 535 sheet: 0.21 (0.25), residues: 500 loop : -1.79 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 220 HIS 0.001 0.000 HIS E 284 PHE 0.018 0.001 PHE A 282 TYR 0.005 0.001 TYR E 245 ARG 0.001 0.000 ARG E 91 *********************** 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 116 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.382 Fit side-chains REVERT: B 226 GLU cc_start: 0.7577 (mp0) cc_final: 0.7206 (mp0) REVERT: D 94 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8311 (mt) REVERT: E 86 ASP cc_start: 0.7850 (m-30) cc_final: 0.7529 (m-30) REVERT: E 282 PHE cc_start: 0.8028 (t80) cc_final: 0.7767 (t80) outliers start: 20 outliers final: 18 residues processed: 115 average time/residue: 0.1725 time to fit residues: 33.2646 Evaluate side-chains 111 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0050 chunk 138 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13115 Z= 0.343 Angle : 0.515 5.596 17815 Z= 0.269 Chirality : 0.048 0.148 1960 Planarity : 0.004 0.031 2250 Dihedral : 9.920 89.546 1920 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.53 % Allowed : 14.33 % Favored : 84.15 % 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: -0.20 (0.22), residues: 1525 helix: 1.37 (0.24), residues: 535 sheet: -0.27 (0.25), residues: 475 loop : -1.54 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 220 HIS 0.003 0.001 HIS B 284 PHE 0.022 0.002 PHE C 282 TYR 0.009 0.001 TYR D 38 ARG 0.002 0.000 ARG A 105 *********************** 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 126 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.304 Fit side-chains REVERT: A 90 LYS cc_start: 0.9094 (pttt) cc_final: 0.8551 (pttm) REVERT: A 245 TYR cc_start: 0.8836 (t80) cc_final: 0.7764 (t80) REVERT: B 226 GLU cc_start: 0.7557 (mp0) cc_final: 0.7240 (mp0) REVERT: C 226 GLU cc_start: 0.7653 (mp0) cc_final: 0.7360 (mp0) REVERT: D 94 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8361 (mt) REVERT: D 245 TYR cc_start: 0.8638 (t80) cc_final: 0.7992 (t80) REVERT: E 86 ASP cc_start: 0.7800 (m-30) cc_final: 0.7474 (m-30) outliers start: 21 outliers final: 16 residues processed: 125 average time/residue: 0.1846 time to fit residues: 37.8850 Evaluate side-chains 117 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 186 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13115 Z= 0.209 Angle : 0.461 4.946 17815 Z= 0.242 Chirality : 0.045 0.140 1960 Planarity : 0.003 0.029 2250 Dihedral : 9.696 89.707 1920 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.53 % Allowed : 14.55 % Favored : 83.93 % 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: -0.03 (0.22), residues: 1525 helix: 1.48 (0.24), residues: 535 sheet: -0.12 (0.25), residues: 475 loop : -1.47 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 220 HIS 0.002 0.001 HIS C 284 PHE 0.045 0.001 PHE D 247 TYR 0.011 0.001 TYR C 245 ARG 0.001 0.000 ARG A 91 ********************** 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 122 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.365 Fit side-chains REVERT: A 90 LYS cc_start: 0.9072 (pttt) cc_final: 0.8542 (pttm) REVERT: B 226 GLU cc_start: 0.7590 (mp0) cc_final: 0.7269 (mp0) REVERT: C 226 GLU cc_start: 0.7610 (mp0) cc_final: 0.7317 (mp0) REVERT: C 270 TYR cc_start: 0.7992 (m-80) cc_final: 0.7660 (m-80) REVERT: D 94 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8336 (mt) REVERT: D 245 TYR cc_start: 0.8570 (t80) cc_final: 0.7913 (t80) REVERT: E 86 ASP cc_start: 0.7861 (m-30) cc_final: 0.7614 (m-30) outliers start: 21 outliers final: 18 residues processed: 121 average time/residue: 0.1818 time to fit residues: 36.0711 Evaluate side-chains 116 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 186 ASN 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: 6.9990 chunk 33 optimal weight: 0.0370 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 0.0040 chunk 86 optimal weight: 5.9990 overall best weight: 2.8076 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.104339 restraints weight = 14215.901| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.58 r_work: 0.3036 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13115 Z= 0.330 Angle : 0.515 5.625 17815 Z= 0.269 Chirality : 0.047 0.148 1960 Planarity : 0.004 0.031 2250 Dihedral : 9.789 88.482 1920 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.75 % Allowed : 14.40 % Favored : 83.85 % 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: -0.14 (0.22), residues: 1525 helix: 1.38 (0.24), residues: 535 sheet: 0.06 (0.25), residues: 505 loop : -1.91 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 220 HIS 0.003 0.001 HIS C 284 PHE 0.043 0.002 PHE D 247 TYR 0.013 0.001 TYR C 245 ARG 0.002 0.000 ARG B 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2270.06 seconds wall clock time: 41 minutes 38.63 seconds (2498.63 seconds total)