Starting phenix.real_space_refine on Sat Apr 6 00:59:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/04_2024/8uny_42421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/04_2024/8uny_42421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/04_2024/8uny_42421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/04_2024/8uny_42421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/04_2024/8uny_42421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/04_2024/8uny_42421_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 P 3 5.49 5 S 36 5.16 5 C 4217 2.51 5 N 1131 2.21 5 O 1159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 219": "NH1" <-> "NH2" Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6546 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 211 Conformer: "B" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 211 bond proxies already assigned to first conformer: 1693 Chain: "B" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2386 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 5, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 149 Chain: "G" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 316 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2110 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 128 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 4.94, per 1000 atoms: 0.75 Number of scatterers: 6546 At special positions: 0 Unit cell: (85.0346, 137.097, 99.7855, 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) S 36 16.00 P 3 15.00 O 1159 8.00 N 1131 7.00 C 4217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 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: 2.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 43.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.564A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.580A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.901A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.710A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.668A pdb=" N VAL A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.780A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) 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 13 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 30 through 60 removed outlier: 3.527A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 67 through 85 removed outlier: 4.528A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.057A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.948A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 210 through 237 removed outlier: 3.986A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 4.038A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.532A pdb=" N ILE R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.611A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.526A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.236A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.044A 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: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.918A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.100A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.758A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.548A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.202A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 897 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: 1.83 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1019 1.32 - 1.44: 1908 1.44 - 1.57: 3709 1.57 - 1.69: 6 1.69 - 1.82: 47 Bond restraints: 6689 Sorted by residual: bond pdb=" C SER R 74 " pdb=" N LEU R 75 " ideal model delta sigma weight residual 1.335 1.398 -0.063 1.30e-02 5.92e+03 2.35e+01 bond pdb=" C LYS A 17 " pdb=" O LYS A 17 " ideal model delta sigma weight residual 1.237 1.291 -0.054 1.17e-02 7.31e+03 2.17e+01 bond pdb=" C GLU A 21 " pdb=" O GLU A 21 " ideal model delta sigma weight residual 1.237 1.289 -0.053 1.17e-02 7.31e+03 2.01e+01 bond pdb=" C PRO R 168 " pdb=" O PRO R 168 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.20e-02 6.94e+03 1.50e+01 bond pdb=" N ILE R 43 " pdb=" CA ILE R 43 " ideal model delta sigma weight residual 1.458 1.504 -0.047 1.41e-02 5.03e+03 1.09e+01 ... (remaining 6684 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.86: 161 106.86 - 113.70: 3766 113.70 - 120.53: 2719 120.53 - 127.37: 2449 127.37 - 134.21: 78 Bond angle restraints: 9173 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 103.32 7.96 1.09e+00 8.42e-01 5.34e+01 angle pdb=" C LYS A 24 " pdb=" N LYS A 25 " pdb=" CA LYS A 25 " ideal model delta sigma weight residual 120.44 111.59 8.85 1.36e+00 5.41e-01 4.24e+01 angle pdb=" N SER R 165 " pdb=" CA SER R 165 " pdb=" C SER R 165 " ideal model delta sigma weight residual 111.14 118.08 -6.94 1.08e+00 8.57e-01 4.13e+01 angle pdb=" C TYR A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta sigma weight residual 121.14 111.68 9.46 1.75e+00 3.27e-01 2.92e+01 angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 105.49 5.79 1.09e+00 8.42e-01 2.82e+01 ... (remaining 9168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 3760 31.95 - 63.89: 76 63.89 - 95.84: 5 95.84 - 127.79: 3 127.79 - 159.73: 3 Dihedral angle restraints: 3847 sinusoidal: 1182 harmonic: 2665 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 168.43 -75.43 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 101.14 159.73 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -44.75 149.34 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 775 0.047 - 0.093: 214 0.093 - 0.140: 84 0.140 - 0.187: 36 0.187 - 0.233: 6 Chirality restraints: 1115 Sorted by residual: chirality pdb=" CA GLN A 12 " pdb=" N GLN A 12 " pdb=" C GLN A 12 " pdb=" CB GLN A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA MET R 171 " pdb=" N MET R 171 " pdb=" C MET R 171 " pdb=" CB MET R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1112 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 215 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C GLU B 215 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU B 215 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 216 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 173 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR B 173 " 0.049 2.00e-02 2.50e+03 pdb=" O THR B 173 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 174 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 11 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C ASP A 11 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP A 11 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN A 12 " -0.016 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1463 2.78 - 3.31: 6232 3.31 - 3.84: 10077 3.84 - 4.37: 10922 4.37 - 4.90: 19744 Nonbonded interactions: 48438 Sorted by model distance: nonbonded pdb=" SG CYS B 271 " pdb=" OD1 ASP B 291 " model vdw 2.255 3.400 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.262 2.520 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.276 2.440 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.331 2.440 nonbonded pdb=" O HIS A 64 " pdb=" C VAL A 65 " model vdw 2.354 3.270 ... (remaining 48433 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 7.530 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.530 Find NCS groups from input model: 0.210 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 0.063 6689 Z= 0.404 Angle : 0.966 9.998 9173 Z= 0.668 Chirality : 0.057 0.233 1115 Planarity : 0.006 0.092 1145 Dihedral : 14.644 159.734 2111 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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 (0.29), residues: 899 helix: 2.35 (0.27), residues: 386 sheet: 0.70 (0.44), residues: 168 loop : -0.76 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 105 HIS 0.009 0.001 HIS R 296 PHE 0.010 0.001 PHE B 234 TYR 0.043 0.001 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.759 Fit side-chains REVERT: A 51 SER cc_start: 0.9275 (p) cc_final: 0.9043 (p) REVERT: A 311 TYR cc_start: 0.9266 (m-80) cc_final: 0.8978 (m-80) REVERT: B 89 LYS cc_start: 0.8742 (mttp) cc_final: 0.8375 (mtmt) REVERT: B 111 TYR cc_start: 0.8649 (m-80) cc_final: 0.8411 (m-80) REVERT: B 254 ASP cc_start: 0.8490 (t70) cc_final: 0.8235 (t0) REVERT: R 232 LYS cc_start: 0.8145 (tppp) cc_final: 0.7942 (ttmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1679 time to fit residues: 23.9097 Evaluate side-chains 70 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6689 Z= 0.199 Angle : 0.523 6.122 9173 Z= 0.283 Chirality : 0.041 0.148 1115 Planarity : 0.004 0.039 1145 Dihedral : 9.473 153.483 998 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.52 % Allowed : 9.93 % Favored : 89.55 % 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: 1.22 (0.29), residues: 899 helix: 2.08 (0.27), residues: 391 sheet: 0.96 (0.43), residues: 170 loop : -0.82 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 158 HIS 0.006 0.001 HIS A 220 PHE 0.010 0.001 PHE B 199 TYR 0.035 0.002 TYR R 185 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.785 Fit side-chains REVERT: A 51 SER cc_start: 0.9256 (p) cc_final: 0.8997 (p) REVERT: B 59 TYR cc_start: 0.8742 (m-10) cc_final: 0.8347 (m-10) REVERT: B 89 LYS cc_start: 0.8800 (mttp) cc_final: 0.8383 (mtpt) REVERT: B 111 TYR cc_start: 0.8664 (m-80) cc_final: 0.7961 (m-80) REVERT: B 254 ASP cc_start: 0.8509 (t70) cc_final: 0.8287 (t0) outliers start: 3 outliers final: 3 residues processed: 84 average time/residue: 0.1871 time to fit residues: 21.4482 Evaluate side-chains 76 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain R residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-dev-5288/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-dev-5288/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-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-dev-5288/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-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-dev-5288/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-dev-5288/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-dev-5288/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-dev-5288/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: 55.232 > 50: distance: 11 - 28: 4.776 distance: 18 - 19: 7.078 distance: 19 - 20: 7.604 distance: 19 - 22: 5.760 distance: 20 - 21: 7.024 distance: 20 - 23: 12.457 distance: 23 - 24: 10.692 distance: 24 - 25: 7.253 distance: 24 - 27: 16.832 distance: 25 - 26: 28.640 distance: 25 - 28: 3.516 distance: 28 - 29: 6.113 distance: 29 - 30: 9.752 distance: 29 - 32: 11.036 distance: 30 - 31: 9.850 distance: 30 - 33: 10.048 distance: 33 - 34: 11.847 distance: 34 - 35: 6.611 distance: 34 - 37: 16.071 distance: 35 - 36: 18.486 distance: 35 - 38: 8.519 distance: 38 - 39: 9.266 distance: 39 - 40: 6.895 distance: 39 - 42: 7.639 distance: 40 - 41: 6.068 distance: 40 - 43: 10.779 distance: 43 - 44: 11.419 distance: 44 - 45: 17.887 distance: 44 - 47: 6.811 distance: 45 - 46: 19.666 distance: 45 - 48: 26.857 distance: 48 - 49: 17.705 distance: 49 - 50: 26.505 distance: 49 - 52: 22.943 distance: 50 - 51: 14.080 distance: 50 - 55: 34.923 distance: 52 - 53: 28.762 distance: 52 - 54: 11.854 distance: 55 - 56: 17.357 distance: 56 - 57: 8.112 distance: 56 - 59: 22.458 distance: 57 - 58: 15.616 distance: 57 - 63: 38.116 distance: 59 - 60: 5.132 distance: 60 - 61: 8.890 distance: 60 - 62: 19.724 distance: 63 - 64: 31.546 distance: 64 - 65: 18.353 distance: 64 - 67: 19.573 distance: 65 - 66: 9.668 distance: 65 - 69: 16.730 distance: 67 - 68: 20.660 distance: 69 - 70: 10.513 distance: 70 - 71: 6.094 distance: 70 - 73: 9.048 distance: 71 - 72: 17.208 distance: 71 - 78: 9.175 distance: 73 - 74: 19.167 distance: 74 - 75: 9.304 distance: 75 - 76: 16.425 distance: 75 - 77: 28.784