Starting phenix.real_space_refine on Fri Dec 8 09:38:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/12_2023/7xtq_33452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/12_2023/7xtq_33452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/12_2023/7xtq_33452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/12_2023/7xtq_33452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/12_2023/7xtq_33452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/12_2023/7xtq_33452_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 Cl 2 4.86 5 C 5066 2.51 5 N 1420 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 109": "OD1" <-> "OD2" Residue "R PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "C" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1910 Chain: "B" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2612 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2090 Unusual residues: {'H8I': 1} Classifications: {'peptide': 273, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 251, None: 1} Not linked: pdbres="ARG R 292 " pdbres="H8I R 401 " Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 380 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG A 380 " occ=0.62 Time building chain proxies: 5.47, per 1000 atoms: 0.68 Number of scatterers: 8010 At special positions: 0 Unit cell: (77.064, 114.582, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 46 16.00 O 1476 8.00 N 1420 7.00 C 5066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " 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: 3.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 37.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 4.409A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.732A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 2 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 'G' and resid 6 through 22 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.423A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 21 through 41 Processing helix chain 'R' and resid 45 through 47 No H-bonds generated for 'chain 'R' and resid 45 through 47' Processing helix chain 'R' and resid 49 through 66 Processing helix chain 'R' and resid 68 through 74 Proline residue: R 72 - end of helix Processing helix chain 'R' and resid 82 through 115 Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 124 through 144 removed outlier: 3.673A pdb=" N GLY R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Proline residue: R 135 - end of helix Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 173 Processing helix chain 'R' and resid 175 through 206 removed outlier: 3.732A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 251 removed outlier: 4.603A pdb=" N GLY R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 262 through 281 Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 285 through 288 No H-bonds generated for 'chain 'R' and resid 285 through 288' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.076A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 46 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.013A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.076A 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: 6.858A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.672A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.955A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.765A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.040A 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: 3.657A 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: 3.929A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.621A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.577A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1069 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: 2.26 Time building geometry restraints manager: 3.35 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: 2581 1.34 - 1.45: 1237 1.45 - 1.57: 4298 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 8181 Sorted by residual: bond pdb=" C1 H8I R 401 " pdb=" N2 H8I R 401 " ideal model delta sigma weight residual 1.352 1.407 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C3 H8I R 401 " pdb=" N1 H8I R 401 " ideal model delta sigma weight residual 1.309 1.355 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C7 H8I R 401 " pdb=" O1 H8I R 401 " ideal model delta sigma weight residual 1.365 1.403 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C7 H8I R 401 " pdb=" C8 H8I R 401 " ideal model delta sigma weight residual 1.390 1.424 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C2 H8I R 401 " pdb=" C3 H8I R 401 " ideal model delta sigma weight residual 1.396 1.424 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 8176 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 217 106.80 - 113.60: 4411 113.60 - 120.40: 3135 120.40 - 127.21: 3241 127.21 - 134.01: 103 Bond angle restraints: 11107 Sorted by residual: angle pdb=" C2 H8I R 401 " pdb=" C1 H8I R 401 " pdb=" N2 H8I R 401 " ideal model delta sigma weight residual 117.71 131.52 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.63 3.57 9.60e-01 1.09e+00 1.39e+01 angle pdb=" N GLN B 9 " pdb=" CA GLN B 9 " pdb=" CB GLN B 9 " ideal model delta sigma weight residual 110.28 115.61 -5.33 1.55e+00 4.16e-01 1.18e+01 angle pdb=" C3 H8I R 401 " pdb=" O1 H8I R 401 " pdb=" C7 H8I R 401 " ideal model delta sigma weight residual 119.25 129.24 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C PRO A 321 " pdb=" N GLU A 322 " pdb=" CA GLU A 322 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 ... (remaining 11102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4501 17.64 - 35.28: 326 35.28 - 52.92: 51 52.92 - 70.55: 9 70.55 - 88.19: 4 Dihedral angle restraints: 4891 sinusoidal: 1920 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.97 42.03 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO B 194 " pdb=" C PRO B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 796 0.037 - 0.074: 307 0.074 - 0.111: 112 0.111 - 0.148: 22 0.148 - 0.185: 5 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA GLN A 31 " pdb=" N GLN A 31 " pdb=" C GLN A 31 " pdb=" CB GLN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 1239 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 134 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO R 135 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 135 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 135 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 228 " -0.181 9.50e-02 1.11e+02 8.14e-02 4.28e+00 pdb=" NE ARG A 228 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 228 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 228 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 228 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO A 321 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.026 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 473 2.73 - 3.27: 7797 3.27 - 3.82: 13099 3.82 - 4.36: 14802 4.36 - 4.90: 26442 Nonbonded interactions: 62613 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.192 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.194 2.440 nonbonded pdb=" O MET B 325 " pdb=" OD1 ASN B 340 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.246 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.273 2.440 ... (remaining 62608 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=0.38 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.910 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.730 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.004 0.055 8181 Z= 0.243 Angle : 0.745 13.809 11107 Z= 0.371 Chirality : 0.046 0.185 1242 Planarity : 0.005 0.081 1431 Dihedral : 12.535 88.193 2966 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1016 helix: 1.49 (0.25), residues: 399 sheet: -0.69 (0.34), residues: 215 loop : -1.79 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 281 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.002 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.008 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.874 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2746 time to fit residues: 70.5102 Evaluate side-chains 182 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 213 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8181 Z= 0.291 Angle : 0.650 11.275 11107 Z= 0.313 Chirality : 0.044 0.173 1242 Planarity : 0.005 0.050 1431 Dihedral : 5.235 64.922 1145 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.18 % Allowed : 10.90 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1016 helix: 1.86 (0.26), residues: 392 sheet: -0.39 (0.34), residues: 218 loop : -1.77 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE N 108 TYR 0.017 0.001 TYR N 60 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 0.903 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 196 average time/residue: 0.2798 time to fit residues: 68.7320 Evaluate side-chains 197 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0755 time to fit residues: 2.0475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8181 Z= 0.186 Angle : 0.589 10.008 11107 Z= 0.280 Chirality : 0.042 0.161 1242 Planarity : 0.004 0.048 1431 Dihedral : 4.943 65.319 1145 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.18 % Allowed : 13.39 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1016 helix: 2.09 (0.26), residues: 393 sheet: -0.40 (0.33), residues: 224 loop : -1.60 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE N 108 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 0.824 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 195 average time/residue: 0.3475 time to fit residues: 87.2988 Evaluate side-chains 191 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1844 time to fit residues: 2.6113 ------------------------------------------------------------------------------- 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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 68.5515 > 50: distance: 35 - 54: 29.690 distance: 39 - 62: 19.117 distance: 46 - 67: 33.534 distance: 49 - 54: 29.255 distance: 54 - 55: 21.106 distance: 55 - 56: 31.613 distance: 55 - 58: 35.361 distance: 56 - 57: 9.873 distance: 56 - 62: 22.474 distance: 58 - 59: 39.400 distance: 59 - 61: 39.252 distance: 62 - 63: 38.343 distance: 63 - 64: 32.543 distance: 63 - 66: 31.387 distance: 64 - 65: 40.184 distance: 64 - 67: 56.103 distance: 67 - 68: 48.780 distance: 68 - 69: 43.636 distance: 68 - 71: 44.684 distance: 69 - 70: 45.017 distance: 69 - 79: 23.782 distance: 71 - 72: 14.811 distance: 77 - 78: 40.683 distance: 80 - 83: 18.412 distance: 81 - 88: 28.524 distance: 83 - 84: 38.372 distance: 84 - 85: 41.076 distance: 85 - 86: 9.888 distance: 85 - 87: 15.474 distance: 88 - 89: 41.192 distance: 89 - 90: 15.302 distance: 89 - 92: 45.596 distance: 90 - 91: 57.543 distance: 90 - 97: 11.561 distance: 92 - 93: 19.962 distance: 93 - 94: 43.187 distance: 94 - 95: 13.953 distance: 94 - 96: 43.663 distance: 97 - 98: 6.716 distance: 98 - 99: 43.818 distance: 99 - 100: 41.240 distance: 99 - 108: 41.241 distance: 103 - 104: 29.379 distance: 104 - 105: 7.713 distance: 105 - 106: 45.700 distance: 105 - 107: 43.163 distance: 108 - 109: 36.957 distance: 108 - 114: 29.436 distance: 109 - 110: 34.220 distance: 109 - 112: 33.203 distance: 110 - 111: 40.185 distance: 110 - 115: 42.739 distance: 112 - 113: 40.647 distance: 113 - 114: 19.067 distance: 115 - 121: 44.768 distance: 116 - 117: 34.269 distance: 116 - 119: 25.366 distance: 117 - 118: 14.623 distance: 117 - 122: 35.787 distance: 119 - 120: 29.756 distance: 120 - 121: 39.769 distance: 122 - 123: 44.173 distance: 123 - 124: 39.026 distance: 123 - 126: 14.349 distance: 124 - 125: 23.938 distance: 124 - 130: 10.691 distance: 126 - 127: 46.543 distance: 127 - 128: 4.973 distance: 127 - 129: 17.992 distance: 130 - 131: 27.127 distance: 131 - 132: 52.273 distance: 132 - 133: 17.781 distance: 132 - 134: 28.377