Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 11:50:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/04_2023/6gdg_4390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/04_2023/6gdg_4390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/04_2023/6gdg_4390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/04_2023/6gdg_4390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/04_2023/6gdg_4390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/04_2023/6gdg_4390_updated.pdb" } resolution = 4.11 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4611 2.51 5 N 1246 2.21 5 O 1317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1913 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2377 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 262 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1721 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 928 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.61 Number of scatterers: 7223 At special positions: 0 Unit cell: (92.02, 125.19, 78.11, 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 49 16.00 O 1317 8.00 N 1246 7.00 C 4611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 2.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 37.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.853A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 58 removed outlier: 3.510A pdb=" N PHE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.791A pdb=" N ILE A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 107 removed outlier: 3.612A pdb=" N ILE A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 187 through 208 Processing helix chain 'A' and resid 225 through 258 removed outlier: 3.782A pdb=" N PHE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.858A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.984A pdb=" N GLN A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.557A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'D' and resid 13 through 39 removed outlier: 3.803A pdb=" N LYS D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 253 through 268 removed outlier: 3.813A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 293 removed outlier: 3.520A pdb=" N LYS D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 322 through 340 removed outlier: 3.546A pdb=" N ILE D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 335 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 380 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.965A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.099A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.630A pdb=" N SER B 147 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.160A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.657A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 327 through 329 removed outlier: 3.657A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 249 through 254 removed outlier: 3.706A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 41 through 44 removed outlier: 3.758A pdb=" N PHE D 212 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.524A pdb=" N PHE D 280 " --> pdb=" O VAL D 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.626A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.549A pdb=" N THR E 122 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 927 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: 1.91 Time building geometry restraints manager: 3.15 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: 2335 1.34 - 1.46: 906 1.46 - 1.58: 4070 1.58 - 1.70: 0 1.70 - 1.81: 65 Bond restraints: 7376 Sorted by residual: bond pdb=" C4 NEC A 400 " pdb=" C5 NEC A 400 " ideal model delta sigma weight residual 1.385 1.474 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C5 NEC A 400 " pdb=" C6 NEC A 400 " ideal model delta sigma weight residual 1.407 1.488 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" CA VAL A 188 " pdb=" CB VAL A 188 " ideal model delta sigma weight residual 1.539 1.560 -0.021 5.40e-03 3.43e+04 1.47e+01 bond pdb=" C8 NEC A 400 " pdb=" N7 NEC A 400 " ideal model delta sigma weight residual 1.302 1.359 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" CA ILE A 64 " pdb=" CB ILE A 64 " ideal model delta sigma weight residual 1.540 1.571 -0.031 1.25e-02 6.40e+03 6.01e+00 ... (remaining 7371 not shown) Histogram of bond angle deviations from ideal: 99.93 - 107.22: 196 107.22 - 114.51: 4180 114.51 - 121.81: 3467 121.81 - 129.10: 2182 129.10 - 136.39: 57 Bond angle restraints: 10082 Sorted by residual: angle pdb=" N ASP D 229 " pdb=" CA ASP D 229 " pdb=" C ASP D 229 " ideal model delta sigma weight residual 112.38 118.19 -5.81 1.22e+00 6.72e-01 2.26e+01 angle pdb=" CA VAL A 188 " pdb=" C VAL A 188 " pdb=" N PRO A 189 " ideal model delta sigma weight residual 120.83 118.29 2.54 6.10e-01 2.69e+00 1.73e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 108.38 113.47 -5.09 1.35e+00 5.49e-01 1.42e+01 angle pdb=" C PHE D 302 " pdb=" N PRO D 303 " pdb=" CA PRO D 303 " ideal model delta sigma weight residual 119.47 123.82 -4.35 1.16e+00 7.43e-01 1.40e+01 angle pdb=" N THR E 104 " pdb=" CA THR E 104 " pdb=" C THR E 104 " ideal model delta sigma weight residual 108.38 113.31 -4.93 1.35e+00 5.49e-01 1.34e+01 ... (remaining 10077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3953 16.99 - 33.99: 251 33.99 - 50.98: 63 50.98 - 67.97: 12 67.97 - 84.96: 4 Dihedral angle restraints: 4283 sinusoidal: 1387 harmonic: 2896 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 146 " pdb=" CB CYS A 146 " ideal model delta sinusoidal sigma weight residual 93.00 177.96 -84.96 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -163.29 77.29 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CA THR B 159 " pdb=" C THR B 159 " pdb=" N SER B 160 " pdb=" CA SER B 160 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 703 0.044 - 0.087: 338 0.087 - 0.131: 105 0.131 - 0.174: 37 0.174 - 0.218: 15 Chirality restraints: 1198 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TRP D 234 " pdb=" N TRP D 234 " pdb=" C TRP D 234 " pdb=" CB TRP D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1195 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 188 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 189 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 284 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 285 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 138 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 139 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.025 5.00e-02 4.00e+02 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2883 2.94 - 3.43: 7414 3.43 - 3.92: 12011 3.92 - 4.41: 13382 4.41 - 4.90: 22757 Nonbonded interactions: 58447 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.449 2.440 nonbonded pdb=" OG1 THR E 104 " pdb=" OD1 ASP E 106 " model vdw 2.471 2.440 nonbonded pdb=" OG SER B 227 " pdb=" OH TYR E 32 " model vdw 2.486 2.440 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.509 2.520 nonbonded pdb=" O GLN D 380 " pdb=" OE1 GLU D 382 " model vdw 2.537 3.040 ... (remaining 58442 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 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: 0.290 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: 1.370 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.420 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.008 0.089 7376 Z= 0.519 Angle : 1.103 9.859 10082 Z= 0.740 Chirality : 0.061 0.218 1198 Planarity : 0.004 0.052 1283 Dihedral : 12.807 79.978 2394 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.89 % Favored : 94.60 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 981 helix: -1.30 (0.21), residues: 357 sheet: -2.83 (0.35), residues: 135 loop : -2.46 (0.23), residues: 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 306 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 315 average time/residue: 0.1926 time to fit residues: 79.5068 Evaluate side-chains 176 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0737 time to fit residues: 1.6545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 19 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS D 361 ASN E 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7376 Z= 0.199 Angle : 0.594 9.604 10082 Z= 0.317 Chirality : 0.043 0.168 1198 Planarity : 0.005 0.068 1283 Dihedral : 4.860 34.019 1060 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.51 (0.24), residues: 981 helix: 0.53 (0.25), residues: 374 sheet: -2.00 (0.32), residues: 191 loop : -1.89 (0.27), residues: 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.1705 time to fit residues: 52.5519 Evaluate side-chains 157 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0704 time to fit residues: 1.2499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 65.0143 > 50: distance: 87 - 91: 10.913 distance: 90 - 146: 28.191 distance: 91 - 92: 13.462 distance: 91 - 97: 30.047 distance: 92 - 93: 22.300 distance: 92 - 95: 22.697 distance: 93 - 94: 53.214 distance: 93 - 98: 16.162 distance: 95 - 96: 24.383 distance: 96 - 97: 34.103 distance: 98 - 99: 24.479 distance: 99 - 100: 6.194 distance: 99 - 102: 14.059 distance: 100 - 101: 23.532 distance: 100 - 103: 42.081 distance: 103 - 104: 31.074 distance: 103 - 109: 9.834 distance: 104 - 105: 26.495 distance: 104 - 107: 30.167 distance: 105 - 106: 4.730 distance: 105 - 110: 14.555 distance: 107 - 108: 27.345 distance: 108 - 109: 17.455 distance: 110 - 111: 7.846 distance: 111 - 114: 4.980 distance: 112 - 113: 4.130 distance: 112 - 121: 11.666 distance: 114 - 115: 3.964 distance: 115 - 116: 5.868 distance: 115 - 117: 8.323 distance: 116 - 118: 12.610 distance: 117 - 119: 14.286 distance: 118 - 120: 12.277 distance: 119 - 120: 16.623 distance: 121 - 122: 15.453 distance: 122 - 123: 24.627 distance: 122 - 125: 9.133 distance: 123 - 124: 12.733 distance: 123 - 128: 10.296 distance: 125 - 126: 8.056 distance: 125 - 127: 13.867 distance: 128 - 129: 23.412 distance: 129 - 130: 14.523 distance: 129 - 132: 25.993 distance: 130 - 131: 22.034 distance: 130 - 133: 20.903 distance: 133 - 134: 11.490 distance: 134 - 135: 7.762 distance: 134 - 137: 32.123 distance: 135 - 136: 6.953 distance: 135 - 141: 5.332 distance: 137 - 138: 38.925 distance: 138 - 139: 17.266 distance: 138 - 140: 23.224 distance: 141 - 142: 13.026 distance: 142 - 143: 17.162 distance: 142 - 145: 12.889 distance: 143 - 144: 20.430 distance: 143 - 147: 19.751 distance: 145 - 146: 16.815 distance: 147 - 148: 5.436 distance: 148 - 149: 24.702 distance: 148 - 151: 6.126 distance: 149 - 150: 18.768 distance: 149 - 158: 23.290 distance: 151 - 152: 10.398 distance: 152 - 153: 7.799 distance: 152 - 154: 8.217 distance: 153 - 155: 8.885 distance: 154 - 156: 4.749 distance: 155 - 157: 3.968 distance: 156 - 157: 6.909 distance: 158 - 159: 17.687 distance: 159 - 160: 5.438 distance: 159 - 162: 18.339 distance: 160 - 161: 10.209 distance: 160 - 166: 29.270 distance: 162 - 163: 6.980 distance: 163 - 164: 4.892 distance: 163 - 165: 11.075