Starting phenix.real_space_refine on Thu Aug 8 03:11:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dq1_27646/08_2024/8dq1_27646_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dq1_27646/08_2024/8dq1_27646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dq1_27646/08_2024/8dq1_27646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dq1_27646/08_2024/8dq1_27646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dq1_27646/08_2024/8dq1_27646_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dq1_27646/08_2024/8dq1_27646_trim.cif" } resolution = 4.1 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4735 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Br 2 7.06 5 P 34 5.49 5 S 52 5.16 5 C 5840 2.51 5 N 1704 2.21 5 O 1779 1.98 5 H 8343 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 12": "OD1" <-> "OD2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B GLU 280": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17754 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3772 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "D" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3728 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "A" Number of atoms: 4749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 4741 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Conformer: "B" Number of residues, atoms: 298, 4741 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} bond proxies already assigned to first conformer: 4787 Chain: "B" Number of atoms: 4733 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 4725 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Conformer: "B" Number of residues, atoms: 298, 4725 Classifications: {'peptide': 298} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} bond proxies already assigned to first conformer: 4771 Chain: "I" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 363 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'K5G': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'K5G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.78, per 1000 atoms: 0.66 Number of scatterers: 17754 At special positions: 0 Unit cell: (77.4, 108.36, 140.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 2 34.99 S 52 16.00 P 34 15.00 O 1779 8.00 N 1704 7.00 C 5840 6.00 H 8343 1.00 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 Atom "HETATM17750 O05 K5G D 301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.10 Conformation dependent library (CDL) restraints added in 2.6 seconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 52.0% alpha, 11.9% beta 6 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 8.28 Creating SS restraints... Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.571A pdb=" N VAL C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.776A pdb=" N LEU C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU C 88 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.205A pdb=" N TRP C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 169 removed outlier: 4.601A pdb=" N GLU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 208 through 224 Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.682A pdb=" N ALA C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.994A pdb=" N GLY D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 81 through 90 removed outlier: 4.263A pdb=" N GLY D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 103 removed outlier: 4.457A pdb=" N GLN D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.885A pdb=" N TRP D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 169 removed outlier: 4.323A pdb=" N GLU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU D 150 " --> pdb=" O PHE D 146 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 160 " --> pdb=" O ARG D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.680A pdb=" N ASP D 194 " --> pdb=" O GLN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.556A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.588A pdb=" N ALA D 231 " --> pdb=" O ASN D 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.588A pdb=" N ALA A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.827A pdb=" N GLY A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.525A pdb=" N LEU A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 removed outlier: 3.738A pdb=" N GLN A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 removed outlier: 4.101A pdb=" N VAL A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.532A pdb=" N GLU A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 232 through 255 Processing helix chain 'A' and resid 257 through 270 removed outlier: 4.049A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.579A pdb=" N GLY A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.539A pdb=" N ALA B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TRP B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 197 through 210 removed outlier: 3.760A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.740A pdb=" N ALA B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 232 through 255 Processing helix chain 'B' and resid 257 through 274 removed outlier: 3.778A pdb=" N LEU B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 273 " --> pdb=" O TRP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 62 Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 62 removed outlier: 3.699A pdb=" N VAL D 94 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 11 removed outlier: 6.693A pdb=" N LEU A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TRP A 34 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LEU A 66 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 36 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL A 90 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 137 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 92 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146 removed outlier: 6.491A pdb=" N HIS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N VAL A 164 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY A 177 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 174 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.507A pdb=" N LEU B 224 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 174 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 166 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 151 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 11 removed outlier: 5.983A pdb=" N GLN B 9 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B 16 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP B 34 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR B 64 " --> pdb=" O TRP B 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 184 429 hydrogen bonds defined for protein. 1223 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 14.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.04: 8318 1.04 - 1.27: 1502 1.27 - 1.49: 4395 1.49 - 1.72: 3748 1.72 - 1.94: 83 Bond restraints: 18046 Sorted by residual: bond pdb=" C12 K5G D 301 " pdb=" C13 K5G D 301 " ideal model delta sigma weight residual 1.520 1.874 -0.354 2.00e-02 2.50e+03 3.13e+02 bond pdb=" C12 K5G C 301 " pdb=" C13 K5G C 301 " ideal model delta sigma weight residual 1.520 1.871 -0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" CA MET C 173 " pdb=" C MET C 173 " ideal model delta sigma weight residual 1.524 1.412 0.111 1.27e-02 6.20e+03 7.70e+01 bond pdb=" C LEU C 130 " pdb=" O LEU C 130 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.20e-02 6.94e+03 6.00e+01 bond pdb=" CA ARG C 37 " pdb=" C ARG C 37 " ideal model delta sigma weight residual 1.522 1.423 0.100 1.38e-02 5.25e+03 5.22e+01 ... (remaining 18041 not shown) Histogram of bond angle deviations from ideal: 92.71 - 101.06: 18 101.06 - 109.41: 11577 109.41 - 117.75: 11774 117.75 - 126.10: 8419 126.10 - 134.45: 444 Bond angle restraints: 32232 Sorted by residual: angle pdb=" N ARG C 36 " pdb=" CA ARG C 36 " pdb=" C ARG C 36 " ideal model delta sigma weight residual 113.12 102.45 10.67 1.25e+00 6.40e-01 7.28e+01 angle pdb=" N LEU C 174 " pdb=" CA LEU C 174 " pdb=" C LEU C 174 " ideal model delta sigma weight residual 113.38 122.22 -8.84 1.23e+00 6.61e-01 5.17e+01 angle pdb=" C PHE A 276 " pdb=" CA PHE A 276 " pdb=" CB PHE A 276 " ideal model delta sigma weight residual 109.27 120.18 -10.91 1.64e+00 3.72e-01 4.43e+01 angle pdb=" N LEU B 117 " pdb=" CA LEU B 117 " pdb=" C LEU B 117 " ideal model delta sigma weight residual 108.23 119.56 -11.33 1.72e+00 3.38e-01 4.34e+01 angle pdb=" N ARG B 114 " pdb=" CA ARG B 114 " pdb=" C ARG B 114 " ideal model delta sigma weight residual 111.28 104.25 7.03 1.09e+00 8.42e-01 4.15e+01 ... (remaining 32227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.73: 7687 26.73 - 53.47: 600 53.47 - 80.20: 151 80.20 - 106.94: 12 106.94 - 133.67: 1 Dihedral angle restraints: 8451 sinusoidal: 4790 harmonic: 3661 Sorted by residual: dihedral pdb=" C PHE A 276 " pdb=" N PHE A 276 " pdb=" CA PHE A 276 " pdb=" CB PHE A 276 " ideal model delta harmonic sigma weight residual -122.60 -139.46 16.86 0 2.50e+00 1.60e-01 4.55e+01 dihedral pdb=" CA GLU C 147 " pdb=" C GLU C 147 " pdb=" N ARG C 148 " pdb=" CA ARG C 148 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CA PHE A 276 " pdb=" CB PHE A 276 " ideal model delta harmonic sigma weight residual 122.80 135.83 -13.03 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 8448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1374 0.123 - 0.245: 55 0.245 - 0.368: 9 0.368 - 0.490: 3 0.490 - 0.613: 2 Chirality restraints: 1443 Sorted by residual: chirality pdb=" CA PHE A 276 " pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CB PHE A 276 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.39e+00 chirality pdb=" CA LEU B 117 " pdb=" N LEU B 117 " pdb=" C LEU B 117 " pdb=" CB LEU B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CA ARG D 156 " pdb=" N ARG D 156 " pdb=" C ARG D 156 " pdb=" CB ARG D 156 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 1440 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 129 " -0.285 2.00e-02 2.50e+03 3.09e-01 1.43e+03 pdb=" CG ASN C 129 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 129 " 0.274 2.00e-02 2.50e+03 pdb=" ND2 ASN C 129 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 129 " 0.449 2.00e-02 2.50e+03 pdb="HD22 ASN C 129 " -0.462 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 115 " -0.204 2.00e-02 2.50e+03 2.41e-01 8.73e+02 pdb=" CD GLN B 115 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN B 115 " 0.195 2.00e-02 2.50e+03 pdb=" NE2 GLN B 115 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 115 " 0.364 2.00e-02 2.50e+03 pdb="HE22 GLN B 115 " -0.370 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 121 " 0.205 2.00e-02 2.50e+03 2.29e-01 7.89e+02 pdb=" CD GLN B 121 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN B 121 " -0.185 2.00e-02 2.50e+03 pdb=" NE2 GLN B 121 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 121 " -0.337 2.00e-02 2.50e+03 pdb="HE22 GLN B 121 " 0.353 2.00e-02 2.50e+03 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.63: 6 1.63 - 2.40: 7039 2.40 - 3.17: 55063 3.17 - 3.93: 74460 3.93 - 4.70: 122223 Warning: very small nonbonded interaction distances. Nonbonded interactions: 258791 Sorted by model distance: nonbonded pdb="HH11 ARG C 37 " pdb="HD23 LEU A 211 " model vdw 0.863 2.270 nonbonded pdb=" HB3 ARG B 43 " pdb="HD23 LEU B 117 " model vdw 1.095 2.440 nonbonded pdb="HG12 VAL D 60 " pdb="BR1 K5G D 301 " model vdw 1.389 3.070 nonbonded pdb="HH11 ARG C 37 " pdb=" CD2 LEU A 211 " model vdw 1.513 2.750 nonbonded pdb=" OE1 GLN B 115 " pdb=" HG3 PRO B 278 " model vdw 1.539 2.620 ... (remaining 258786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 59 or resid 61 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2)) or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 244 or resid 246 through 254 or \ (resid 255 and (name N or name CA or name C or name O )) or resid 256 through 2 \ 98)) selection = (chain 'B' and (resid 1 through 59 or resid 61 through 230 or (resid 231 and (na \ me N or name CA or name C or name O or name CB )) or resid 232 through 244 or re \ sid 246 through 298)) } ncs_group { reference = (chain 'C' and (resid 4 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or resid 51 through 68 or (resid \ 69 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or resid 70 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)) or resid 131 thr \ ough 155 or (resid 156 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 157 \ through 161 or (resid 162 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or resid 163 through 211 or (resid 212 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or r \ esid 213 through 241 or resid 301)) selection = (chain 'D' and (resid 4 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 \ or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 11 through 35 or (res \ id 36 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name NE or name CZ or name NH1 or name NH2)) or resid 37 or (resid 38 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or resid 39 through 173 or (resid 174 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or resid 175 through 241 \ or resid 301)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.250 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 68.030 Find NCS groups from input model: 0.550 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.011 0.354 9703 Z= 0.659 Angle : 1.104 11.602 13309 Z= 0.600 Chirality : 0.065 0.613 1443 Planarity : 0.007 0.086 1599 Dihedral : 19.210 133.673 3695 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.87 % Allowed : 1.52 % Favored : 97.61 % Cbeta Deviations : 0.30 % 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: -1.40 (0.25), residues: 1069 helix: 0.07 (0.23), residues: 482 sheet: -1.96 (0.40), residues: 144 loop : -1.60 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 100 HIS 0.020 0.003 HIS B 74 PHE 0.037 0.003 PHE A 25 TYR 0.041 0.004 TYR B 201 ARG 0.033 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 302 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASP cc_start: 0.7948 (m-30) cc_final: 0.7590 (m-30) REVERT: C 55 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7300 (ttm110) REVERT: C 75 GLN cc_start: 0.7361 (mt0) cc_final: 0.6917 (mt0) REVERT: C 76 ASN cc_start: 0.8454 (t0) cc_final: 0.8175 (t0) REVERT: C 85 LEU cc_start: 0.8336 (mt) cc_final: 0.8097 (mt) REVERT: C 109 ASN cc_start: 0.7980 (m110) cc_final: 0.7630 (m-40) REVERT: C 142 ASN cc_start: 0.7395 (m110) cc_final: 0.7098 (t0) REVERT: C 218 ASN cc_start: 0.7852 (m110) cc_final: 0.7600 (m110) REVERT: D 55 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7708 (tmm160) REVERT: D 74 MET cc_start: 0.7536 (mmt) cc_final: 0.7256 (mmm) REVERT: D 76 ASN cc_start: 0.8728 (t0) cc_final: 0.8408 (t0) REVERT: D 77 TYR cc_start: 0.7363 (m-80) cc_final: 0.5795 (m-80) REVERT: D 106 MET cc_start: 0.4932 (tmm) cc_final: 0.4706 (tpp) REVERT: D 107 LEU cc_start: 0.7668 (mm) cc_final: 0.7429 (tp) REVERT: D 109 ASN cc_start: 0.7576 (m-40) cc_final: 0.7259 (m110) REVERT: D 147 GLU cc_start: 0.8012 (tt0) cc_final: 0.7591 (tt0) REVERT: D 156 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6875 (ttm-80) REVERT: D 214 PHE cc_start: 0.7954 (t80) cc_final: 0.7541 (t80) REVERT: A 13 ASP cc_start: 0.8533 (p0) cc_final: 0.8094 (p0) REVERT: A 122 ARG cc_start: 0.7441 (mpp80) cc_final: 0.7230 (mtt90) REVERT: A 144 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8518 (mm-30) REVERT: A 161 ASP cc_start: 0.8461 (m-30) cc_final: 0.8099 (m-30) REVERT: A 256 GLU cc_start: 0.5493 (tt0) cc_final: 0.4896 (mt-10) REVERT: A 276 PHE cc_start: 0.8958 (p90) cc_final: 0.8742 (p90) REVERT: A 289 MET cc_start: 0.8645 (ttt) cc_final: 0.8430 (ttp) REVERT: B 167 TYR cc_start: 0.7656 (t80) cc_final: 0.7339 (t80) REVERT: B 264 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6935 (tt0) outliers start: 8 outliers final: 4 residues processed: 305 average time/residue: 0.4917 time to fit residues: 203.0395 Evaluate side-chains 263 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 258 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: