Starting phenix.real_space_refine (version: 1.21rc1) on Thu May 4 03:01:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/05_2023/7xk2_33241_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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 66 5.16 5 C 5594 2.51 5 N 1509 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 190": "OE1" <-> "OE2" Residue "R ASP 273": "OD1" <-> "OD2" Residue "R PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 137": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 8791 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2229 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "S" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1711 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 429 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.57 Number of scatterers: 8791 At special positions: 0 Unit cell: (87.36, 116.48, 132.08, 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 66 16.00 O 1622 8.00 N 1509 7.00 C 5594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 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: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 31.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.655A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'R' and resid 26 through 52 Proline residue: R 31 - end of helix removed outlier: 3.966A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 79 removed outlier: 3.894A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 85 No H-bonds generated for 'chain 'R' and resid 82 through 85' Processing helix chain 'R' and resid 98 through 129 removed outlier: 4.038A pdb=" N LEU R 104 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE R 105 " --> pdb=" O ARG R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 157 Processing helix chain 'R' and resid 160 through 164 removed outlier: 3.989A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 217 removed outlier: 3.808A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.589A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG R 210 " --> pdb=" O PHE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 260 removed outlier: 3.843A pdb=" N ILE R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 289 removed outlier: 4.213A pdb=" N ASP R 273 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU R 274 " --> pdb=" O SER R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 293 No H-bonds generated for 'chain 'R' and resid 291 through 293' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'A' and resid 220 through 224 removed outlier: 6.772A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.759A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.007A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.739A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.540A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.836A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.623A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.849A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 18 through 23 Processing sheet with id= J, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= K, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= L, first strand: chain 'S' and resid 156 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 5.813A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 921 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: 2.35 Time building geometry restraints manager: 3.63 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: 2528 1.34 - 1.46: 1693 1.46 - 1.57: 4662 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 8981 Sorted by residual: bond pdb=" C20 FI7 R 401 " pdb=" C21 FI7 R 401 " ideal model delta sigma weight residual 1.598 1.349 0.249 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C26 FI7 R 401 " pdb=" C27 FI7 R 401 " ideal model delta sigma weight residual 1.359 1.520 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C25 FI7 R 401 " pdb=" C26 FI7 R 401 " ideal model delta sigma weight residual 1.653 1.525 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C27 FI7 R 401 " pdb=" C28 FI7 R 401 " ideal model delta sigma weight residual 1.658 1.536 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C07 FI7 R 401 " pdb=" N06 FI7 R 401 " ideal model delta sigma weight residual 1.336 1.422 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 8976 not shown) Histogram of bond angle deviations from ideal: 93.56 - 101.68: 29 101.68 - 109.80: 1220 109.80 - 117.92: 5379 117.92 - 126.05: 5361 126.05 - 134.17: 172 Bond angle restraints: 12161 Sorted by residual: angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 124.36 -10.26 2.00e+00 2.50e-01 2.63e+01 angle pdb=" C ALA R 174 " pdb=" N ASN R 175 " pdb=" CA ASN R 175 " ideal model delta sigma weight residual 122.46 129.13 -6.67 1.41e+00 5.03e-01 2.23e+01 angle pdb=" CA LYS C 20 " pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" C THR R 283 " pdb=" N TYR R 284 " pdb=" CA TYR R 284 " ideal model delta sigma weight residual 121.58 112.72 8.86 1.95e+00 2.63e-01 2.07e+01 angle pdb=" CA TYR R 284 " pdb=" CB TYR R 284 " pdb=" CG TYR R 284 " ideal model delta sigma weight residual 113.90 121.60 -7.70 1.80e+00 3.09e-01 1.83e+01 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 5100 32.11 - 64.21: 196 64.21 - 96.32: 14 96.32 - 128.42: 0 128.42 - 160.53: 1 Dihedral angle restraints: 5311 sinusoidal: 2045 harmonic: 3266 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 160.11 -67.11 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -35.39 -50.61 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA TYR S 94 " pdb=" C TYR S 94 " pdb=" N TYR S 95 " pdb=" CA TYR S 95 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1255 0.100 - 0.199: 99 0.199 - 0.298: 8 0.298 - 0.398: 1 0.398 - 0.497: 1 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CB ILE R 238 " pdb=" CA ILE R 238 " pdb=" CG1 ILE R 238 " pdb=" CG2 ILE R 238 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CG LEU R 80 " pdb=" CB LEU R 80 " pdb=" CD1 LEU R 80 " pdb=" CD2 LEU R 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR R 284 " pdb=" N TYR R 284 " pdb=" C TYR R 284 " pdb=" CB TYR R 284 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1361 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 265 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C ILE A 265 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 265 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 266 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " 0.191 9.50e-02 1.11e+02 8.64e-02 5.90e+00 pdb=" NE ARG B 134 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " -0.181 9.50e-02 1.11e+02 8.18e-02 5.17e+00 pdb=" NE ARG B 197 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1917 2.78 - 3.31: 7760 3.31 - 3.84: 14885 3.84 - 4.37: 17158 4.37 - 4.90: 29664 Nonbonded interactions: 71384 Sorted by model distance: nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.251 2.440 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.291 2.440 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.297 2.440 nonbonded pdb=" OG SER S 206 " pdb=" O THR S 213 " model vdw 2.313 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 2.440 ... (remaining 71379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.350 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.006 0.249 8981 Z= 0.447 Angle : 1.027 13.801 12161 Z= 0.517 Chirality : 0.056 0.497 1364 Planarity : 0.007 0.086 1542 Dihedral : 16.706 160.527 3192 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.32 % 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: -2.41 (0.23), residues: 1114 helix: -1.04 (0.25), residues: 355 sheet: -1.11 (0.30), residues: 265 loop : -2.24 (0.25), residues: 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.054 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 172 average time/residue: 0.2469 time to fit residues: 56.8023 Evaluate side-chains 168 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0847 time to fit residues: 1.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 0.0470 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 8981 Z= 0.154 Angle : 0.581 8.009 12161 Z= 0.296 Chirality : 0.041 0.176 1364 Planarity : 0.004 0.044 1542 Dihedral : 6.819 159.268 1226 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 2.25 % 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 (0.24), residues: 1114 helix: 0.26 (0.27), residues: 351 sheet: -1.21 (0.29), residues: 277 loop : -2.15 (0.26), residues: 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.025 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 184 average time/residue: 0.2264 time to fit residues: 56.3188 Evaluate side-chains 174 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0903 time to fit residues: 3.5865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 0.0070 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8981 Z= 0.219 Angle : 0.601 11.053 12161 Z= 0.304 Chirality : 0.042 0.232 1364 Planarity : 0.004 0.042 1542 Dihedral : 6.760 160.423 1226 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 2.25 % 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: -1.32 (0.24), residues: 1114 helix: 0.72 (0.28), residues: 354 sheet: -1.26 (0.29), residues: 266 loop : -1.82 (0.26), residues: 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.111 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 184 average time/residue: 0.2664 time to fit residues: 65.3973 Evaluate side-chains 169 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1181 time to fit residues: 3.4111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0045 > 50: distance: 100 - 107: 16.754 distance: 107 - 108: 24.610 distance: 108 - 109: 19.318 distance: 108 - 111: 16.031 distance: 109 - 110: 19.509 distance: 109 - 112: 11.488 distance: 112 - 113: 26.544 distance: 113 - 114: 22.191 distance: 113 - 116: 11.234 distance: 114 - 115: 5.580 distance: 114 - 120: 17.123 distance: 116 - 117: 33.512 distance: 117 - 118: 13.094 distance: 120 - 121: 23.308 distance: 121 - 122: 20.509 distance: 121 - 124: 12.445 distance: 122 - 123: 44.485 distance: 122 - 131: 4.602 distance: 124 - 125: 13.685 distance: 125 - 126: 22.618 distance: 126 - 127: 26.512 distance: 127 - 128: 11.888 distance: 128 - 129: 5.556 distance: 128 - 130: 10.531 distance: 131 - 132: 33.652 distance: 132 - 133: 23.295 distance: 132 - 135: 6.824 distance: 133 - 134: 23.634 distance: 133 - 136: 38.213 distance: 136 - 137: 18.146 distance: 137 - 138: 3.247 distance: 138 - 139: 13.318 distance: 138 - 140: 15.242 distance: 140 - 141: 11.127 distance: 141 - 142: 18.692 distance: 141 - 144: 28.871 distance: 142 - 143: 21.360 distance: 142 - 147: 36.812 distance: 144 - 145: 13.498 distance: 144 - 146: 17.971 distance: 148 - 149: 10.859 distance: 148 - 151: 32.721 distance: 149 - 150: 41.412 distance: 149 - 155: 3.817 distance: 151 - 152: 33.814 distance: 152 - 153: 24.286 distance: 152 - 154: 13.878 distance: 155 - 156: 16.431 distance: 156 - 157: 12.049 distance: 156 - 159: 44.144 distance: 157 - 158: 37.766 distance: 157 - 160: 10.772 distance: 160 - 161: 17.126 distance: 161 - 162: 12.420 distance: 162 - 163: 34.415 distance: 164 - 165: 18.956 distance: 165 - 166: 4.930 distance: 165 - 168: 22.485 distance: 166 - 167: 7.872 distance: 166 - 174: 21.393 distance: 168 - 169: 6.901 distance: 169 - 170: 34.079 distance: 169 - 171: 22.473 distance: 170 - 172: 7.772 distance: 171 - 173: 23.458 distance: 172 - 173: 38.909