Starting phenix.real_space_refine on Fri Jan 19 20:12:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d64_27216/01_2024/8d64_27216_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d64_27216/01_2024/8d64_27216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d64_27216/01_2024/8d64_27216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d64_27216/01_2024/8d64_27216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d64_27216/01_2024/8d64_27216_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d64_27216/01_2024/8d64_27216_updated.pdb" } resolution = 3.14 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 8175 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12545 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.55 Number of scatterers: 12545 At special positions: 0 Unit cell: (90.2, 90.2, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 2250 8.00 N 2085 7.00 C 8175 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: 4.46 Conformation dependent library (CDL) restraints added in 2.6 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 29.9% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 222 removed outlier: 3.863A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 248 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 222 removed outlier: 3.863A pdb=" N VAL B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 222 removed outlier: 3.863A pdb=" N VAL C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 248 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 261 through 285 Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 222 removed outlier: 3.864A pdb=" N VAL D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 248 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 261 through 285 Processing helix chain 'D' and resid 303 through 316 Processing helix chain 'E' and resid 63 through 68 Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 222 removed outlier: 3.863A pdb=" N VAL E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 248 Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 303 through 316 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.849A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 40 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A 18 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN A 42 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL A 16 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR A 44 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL A 14 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 147 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.072A 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 58 removed outlier: 6.849A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 40 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 18 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN B 42 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL B 16 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR B 44 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL B 14 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 147 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 7.070A 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 58 removed outlier: 6.847A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL C 40 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE C 18 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN C 42 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL C 16 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR C 44 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL C 14 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL C 147 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.071A 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 58 removed outlier: 6.848A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL D 40 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE D 18 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN D 42 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL D 16 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR D 44 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL D 14 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL D 147 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.071A 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 58 removed outlier: 6.848A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL E 40 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE E 18 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN E 42 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL E 16 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR E 44 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL E 14 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL E 147 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.071A 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 174 540 hydrogen bonds defined for protein. 1590 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: 3.34 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3947 1.34 - 1.46: 2403 1.46 - 1.57: 6475 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 12880 Sorted by residual: bond pdb=" N ASP D 158 " pdb=" CA ASP D 158 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.20e+01 bond pdb=" N ASP E 158 " pdb=" CA ASP E 158 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.19e+01 bond pdb=" N ASP A 158 " pdb=" CA ASP A 158 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.15e+01 bond pdb=" N ASP B 158 " pdb=" CA ASP B 158 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.11e+01 bond pdb=" N ASP C 158 " pdb=" CA ASP C 158 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.08e+01 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.82: 395 106.82 - 113.68: 6951 113.68 - 120.55: 5248 120.55 - 127.41: 4786 127.41 - 134.27: 165 Bond angle restraints: 17545 Sorted by residual: angle pdb=" C ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta sigma weight residual 116.54 110.76 5.78 1.46e+00 4.69e-01 1.57e+01 angle pdb=" C ASP E 158 " pdb=" CA ASP E 158 " pdb=" CB ASP E 158 " ideal model delta sigma weight residual 116.54 110.79 5.75 1.46e+00 4.69e-01 1.55e+01 angle pdb=" C ASP C 158 " pdb=" CA ASP C 158 " pdb=" CB ASP C 158 " ideal model delta sigma weight residual 116.54 110.80 5.74 1.46e+00 4.69e-01 1.55e+01 angle pdb=" C ASP A 158 " pdb=" CA ASP A 158 " pdb=" CB ASP A 158 " ideal model delta sigma weight residual 116.54 110.81 5.73 1.46e+00 4.69e-01 1.54e+01 angle pdb=" C ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta sigma weight residual 116.54 110.82 5.72 1.46e+00 4.69e-01 1.54e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 6702 16.95 - 33.89: 703 33.89 - 50.84: 100 50.84 - 67.78: 15 67.78 - 84.73: 10 Dihedral angle restraints: 7530 sinusoidal: 3025 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 -151.43 -28.57 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA LEU E 118 " pdb=" C LEU E 118 " pdb=" N PHE E 119 " pdb=" CA PHE E 119 " ideal model delta harmonic sigma weight residual -180.00 -151.45 -28.55 0 5.00e+00 4.00e-02 3.26e+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 -151.45 -28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1323 0.050 - 0.100: 453 0.100 - 0.150: 137 0.150 - 0.200: 26 0.200 - 0.250: 11 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU A 156 " pdb=" N GLU A 156 " pdb=" C GLU A 156 " pdb=" CB GLU A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA GLU E 156 " pdb=" N GLU E 156 " pdb=" C GLU E 156 " pdb=" CB GLU E 156 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 54 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 55 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 54 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO C 55 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 54 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO E 55 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.033 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3294 2.80 - 3.32: 10450 3.32 - 3.85: 20071 3.85 - 4.37: 24148 4.37 - 4.90: 43075 Nonbonded interactions: 101038 Sorted by model distance: nonbonded pdb=" OE2 GLU A 59 " pdb=" OG SER B 134 " model vdw 2.275 2.440 nonbonded pdb=" OG SER A 227 " pdb=" CG GLU A 230 " model vdw 2.289 3.440 nonbonded pdb=" OG SER C 227 " pdb=" CG GLU C 230 " model vdw 2.289 3.440 nonbonded pdb=" OG SER E 227 " pdb=" CG GLU E 230 " model vdw 2.289 3.440 nonbonded pdb=" OG SER B 227 " pdb=" CG GLU B 230 " model vdw 2.289 3.440 ... (remaining 101033 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.940 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.340 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.007 0.045 12880 Z= 0.458 Angle : 0.809 7.624 17545 Z= 0.470 Chirality : 0.058 0.250 1950 Planarity : 0.006 0.059 2235 Dihedral : 13.690 84.726 4620 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % 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: -3.61 (0.18), residues: 1525 helix: -1.79 (0.18), residues: 535 sheet: -1.46 (0.22), residues: 505 loop : -3.92 (0.20), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 206 HIS 0.005 0.001 HIS D 177 PHE 0.014 0.002 PHE C 106 TYR 0.016 0.002 TYR B 245 ARG 0.003 0.000 ARG E 123 *********************** 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 196 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.447 Fit side-chains REVERT: B 38 TYR cc_start: 0.8893 (m-80) cc_final: 0.8508 (m-80) REVERT: B 131 GLU cc_start: 0.8794 (tt0) cc_final: 0.8481 (tt0) REVERT: C 38 TYR cc_start: 0.8912 (m-80) cc_final: 0.8611 (m-80) REVERT: C 90 LYS cc_start: 0.8893 (pttt) cc_final: 0.8600 (pttm) REVERT: C 146 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7878 (mm-40) REVERT: D 38 TYR cc_start: 0.8771 (m-80) cc_final: 0.8506 (m-80) REVERT: E 65 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8266 (mtm110) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2852 time to fit residues: 77.1031 Evaluate side-chains 121 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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: 0.7980 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 182 GLN A 233 GLN B 139 GLN C 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12880 Z= 0.170 Angle : 0.532 5.744 17545 Z= 0.279 Chirality : 0.046 0.146 1950 Planarity : 0.004 0.046 2235 Dihedral : 4.975 21.965 1690 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.55 % Allowed : 11.93 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.20), residues: 1525 helix: -0.30 (0.21), residues: 535 sheet: -0.62 (0.27), residues: 395 loop : -3.00 (0.21), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 206 HIS 0.005 0.001 HIS C 177 PHE 0.012 0.001 PHE D 247 TYR 0.011 0.001 TYR A 245 ARG 0.009 0.000 ARG B 123 *********************** 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 186 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.304 Fit side-chains REVERT: A 245 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6574 (t80) REVERT: B 38 TYR cc_start: 0.8868 (m-80) cc_final: 0.8580 (m-80) REVERT: C 38 TYR cc_start: 0.8854 (m-80) cc_final: 0.8526 (m-80) REVERT: C 90 LYS cc_start: 0.8867 (pttt) cc_final: 0.8573 (pttm) REVERT: C 146 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7838 (mm-40) REVERT: D 38 TYR cc_start: 0.8748 (m-80) cc_final: 0.8475 (m-80) REVERT: D 65 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7888 (mtm110) REVERT: E 65 ARG cc_start: 0.8498 (mtp-110) cc_final: 0.8252 (mtm110) REVERT: E 245 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.6778 (t80) outliers start: 35 outliers final: 26 residues processed: 175 average time/residue: 0.2474 time to fit residues: 62.4332 Evaluate side-chains 162 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 304 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 0.2980 chunk 121 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 GLN E 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1489 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: