Starting phenix.real_space_refine on Fri Apr 5 21:36:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/04_2024/8uo4_42427_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/04_2024/8uo4_42427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/04_2024/8uo4_42427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/04_2024/8uo4_42427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/04_2024/8uo4_42427_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/04_2024/8uo4_42427_updated.pdb" } resolution = 4.0 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= 0.015 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 16 5.16 5 C 3576 2.51 5 N 1034 2.21 5 O 1072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5702 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 1854 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 7, 'TRANS': 284} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 610 Unresolved non-hydrogen angles: 758 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 13, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 392 Chain: "B" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2224 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 20, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 241 Chain: "G" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 307 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1269 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 309 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Time building chain proxies: 3.84, per 1000 atoms: 0.67 Number of scatterers: 5702 At special positions: 0 Unit cell: (85.0346, 137.097, 100.653, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 3 15.00 Mg 1 11.99 O 1072 8.00 N 1034 7.00 C 3576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 10 sheets defined 41.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.915A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.726A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.601A pdb=" N ASN A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.505A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.561A pdb=" N ASN A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 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 332 through 351 removed outlier: 3.643A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.189A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (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 12 through 23 Processing helix chain 'G' and resid 33 through 43 Processing helix chain 'R' and resid 37 through 54 removed outlier: 3.744A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 92 removed outlier: 4.016A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.631A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.852A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.569A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.709A 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 184 removed outlier: 3.927A pdb=" N ASN R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 179 through 184' Processing helix chain 'R' and resid 199 through 207 Processing helix chain 'R' and resid 210 through 233 removed outlier: 4.021A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 295 removed outlier: 4.040A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 305 through 325 removed outlier: 3.566A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU R 310 " --> pdb=" O GLU R 306 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 removed outlier: 7.033A pdb=" N ALA A 243 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE A 246 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE A 288 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 248 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A 290 " --> pdb=" O VAL A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.531A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 78 through 81 removed outlier: 3.817A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 113 Processing sheet with id= E, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.721A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.039A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.723A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 306 through 309 removed outlier: 3.860A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.615A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.207A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 750 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: 1.53 Time building geometry restraints manager: 2.33 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: 1959 1.34 - 1.46: 1163 1.46 - 1.58: 2638 1.58 - 1.69: 5 1.69 - 1.81: 20 Bond restraints: 5785 Sorted by residual: bond pdb=" N ILE A 383 " pdb=" CA ILE A 383 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.09e-02 8.42e+03 1.27e+01 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.00e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" N MET A 386 " pdb=" CA MET A 386 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.16e+00 bond pdb=" N ARG A 380 " pdb=" CA ARG A 380 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.06e+00 ... (remaining 5780 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.37: 152 107.37 - 114.36: 3337 114.36 - 121.35: 2917 121.35 - 128.34: 1514 128.34 - 135.32: 44 Bond angle restraints: 7964 Sorted by residual: angle pdb=" N ILE A 383 " pdb=" CA ILE A 383 " pdb=" C ILE A 383 " ideal model delta sigma weight residual 111.88 102.30 9.58 1.06e+00 8.90e-01 8.17e+01 angle pdb=" N ASN A 377 " pdb=" CA ASN A 377 " pdb=" C ASN A 377 " ideal model delta sigma weight residual 111.71 105.31 6.40 1.15e+00 7.56e-01 3.09e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 135.32 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA GLN A 390 " pdb=" C GLN A 390 " pdb=" O GLN A 390 " ideal model delta sigma weight residual 121.84 116.75 5.09 1.16e+00 7.43e-01 1.92e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 109.96 103.66 6.30 1.49e+00 4.50e-01 1.79e+01 ... (remaining 7959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 3274 29.19 - 58.39: 51 58.39 - 87.58: 3 87.58 - 116.77: 1 116.77 - 145.97: 1 Dihedral angle restraints: 3330 sinusoidal: 687 harmonic: 2643 Sorted by residual: 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 -41.37 145.97 1 2.00e+01 2.50e-03 4.39e+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 260.87 150.85 110.02 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA CYS A 237 " pdb=" C CYS A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 883 0.067 - 0.133: 100 0.133 - 0.200: 5 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 992 Sorted by residual: chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 382 " pdb=" N ILE A 382 " pdb=" C ILE A 382 " pdb=" CB ILE A 382 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 989 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 376 " 0.012 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C PHE A 376 " -0.044 2.00e-02 2.50e+03 pdb=" O PHE A 376 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 377 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE A 382 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO G 49 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.021 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2045 2.84 - 3.35: 5354 3.35 - 3.87: 8437 3.87 - 4.38: 8611 4.38 - 4.90: 15002 Nonbonded interactions: 39449 Sorted by model distance: nonbonded pdb=" O SER G 31 " pdb=" OG SER G 31 " model vdw 2.322 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.345 2.440 nonbonded pdb=" OG SER A 54 " pdb=" OD2 ASP A 223 " model vdw 2.369 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.371 2.440 nonbonded pdb=" O GLY B 141 " pdb=" NE2 GLN B 176 " model vdw 2.374 2.520 ... (remaining 39444 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: 1.490 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: 7.490 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.530 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 0.052 5785 Z= 0.287 Angle : 0.716 14.824 7964 Z= 0.406 Chirality : 0.045 0.333 992 Planarity : 0.003 0.037 1040 Dihedral : 11.999 145.967 1598 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.04 (0.29), residues: 870 helix: 1.82 (0.28), residues: 353 sheet: -1.40 (0.42), residues: 159 loop : -1.25 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.002 HIS B 54 PHE 0.012 0.001 PHE B 235 TYR 0.005 0.001 TYR B 105 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.654 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1409 time to fit residues: 16.7606 Evaluate side-chains 58 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5785 Z= 0.211 Angle : 0.493 6.250 7964 Z= 0.268 Chirality : 0.041 0.140 992 Planarity : 0.003 0.036 1040 Dihedral : 6.975 138.910 958 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.05 % Allowed : 10.06 % Favored : 86.89 % 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: 0.04 (0.29), residues: 870 helix: 1.74 (0.28), residues: 363 sheet: -1.18 (0.44), residues: 145 loop : -1.23 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS B 54 PHE 0.014 0.001 PHE B 292 TYR 0.018 0.001 TYR B 124 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.539 Fit side-chains REVERT: B 339 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.8325 (m-10) REVERT: G 41 CYS cc_start: 0.8211 (m) cc_final: 0.7864 (p) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.0914 time to fit residues: 9.9754 Evaluate side-chains 65 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5785 Z= 0.142 Angle : 0.432 5.957 7964 Z= 0.232 Chirality : 0.039 0.129 992 Planarity : 0.003 0.033 1040 Dihedral : 6.370 130.425 958 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.44 % Allowed : 12.50 % Favored : 85.06 % 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: 0.26 (0.29), residues: 870 helix: 2.07 (0.28), residues: 361 sheet: -1.05 (0.41), residues: 155 loop : -1.27 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 234 HIS 0.005 0.001 HIS B 54 PHE 0.014 0.001 PHE B 292 TYR 0.014 0.001 TYR B 124 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.697 Fit side-chains REVERT: B 234 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: G 41 CYS cc_start: 0.8183 (m) cc_final: 0.7806 (p) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.0928 time to fit residues: 9.9124 Evaluate side-chains 66 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 0.0050 chunk 9 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 0.0170 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 overall best weight: 0.5234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5785 Z= 0.110 Angle : 0.412 5.917 7964 Z= 0.219 Chirality : 0.039 0.127 992 Planarity : 0.002 0.030 1040 Dihedral : 5.979 123.166 958 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.66 % Allowed : 14.33 % Favored : 82.01 % 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: 0.46 (0.29), residues: 870 helix: 2.26 (0.28), residues: 363 sheet: -1.03 (0.41), residues: 162 loop : -1.16 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 234 HIS 0.002 0.001 HIS B 54 PHE 0.011 0.001 PHE B 292 TYR 0.011 0.001 TYR B 124 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.657 Fit side-chains REVERT: A 234 TRP cc_start: 0.8301 (p90) cc_final: 0.8096 (p-90) REVERT: B 234 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: B 339 TRP cc_start: 0.8513 (m100) cc_final: 0.8095 (m-10) REVERT: G 41 CYS cc_start: 0.8139 (m) cc_final: 0.7786 (p) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.1067 time to fit residues: 12.5941 Evaluate side-chains 72 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 17 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5785 Z= 0.142 Angle : 0.422 5.845 7964 Z= 0.224 Chirality : 0.039 0.126 992 Planarity : 0.002 0.031 1040 Dihedral : 5.867 119.943 958 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.27 % Allowed : 15.24 % Favored : 80.49 % 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: 0.58 (0.29), residues: 870 helix: 2.37 (0.28), residues: 364 sheet: -0.96 (0.41), residues: 162 loop : -1.13 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 292 TYR 0.007 0.001 TYR A 360 ARG 0.001 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.605 Fit side-chains REVERT: A 234 TRP cc_start: 0.8400 (p90) cc_final: 0.8187 (p-90) REVERT: B 234 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: B 339 TRP cc_start: 0.8532 (m100) cc_final: 0.8070 (m-10) REVERT: G 41 CYS cc_start: 0.8214 (m) cc_final: 0.7794 (p) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.0960 time to fit residues: 11.2864 Evaluate side-chains 74 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 87 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.028 5785 Z= 0.102 Angle : 0.401 6.249 7964 Z= 0.211 Chirality : 0.039 0.125 992 Planarity : 0.002 0.030 1040 Dihedral : 5.564 113.747 958 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.27 % Allowed : 15.55 % Favored : 80.18 % 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: 0.75 (0.30), residues: 870 helix: 2.51 (0.28), residues: 363 sheet: -0.68 (0.43), residues: 157 loop : -1.12 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.002 0.001 HIS B 225 PHE 0.009 0.001 PHE A 212 TYR 0.004 0.000 TYR R 174 ARG 0.001 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.689 Fit side-chains REVERT: B 234 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: B 339 TRP cc_start: 0.8492 (m100) cc_final: 0.8069 (m-10) REVERT: G 41 CYS cc_start: 0.8148 (m) cc_final: 0.7747 (p) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.0935 time to fit residues: 11.2243 Evaluate side-chains 73 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5785 Z= 0.119 Angle : 0.415 8.021 7964 Z= 0.216 Chirality : 0.039 0.123 992 Planarity : 0.002 0.029 1040 Dihedral : 5.429 109.849 958 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.96 % Allowed : 17.07 % Favored : 78.96 % 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: 0.86 (0.30), residues: 870 helix: 2.60 (0.28), residues: 361 sheet: -0.57 (0.45), residues: 147 loop : -1.08 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 234 HIS 0.002 0.001 HIS B 225 PHE 0.009 0.001 PHE B 292 TYR 0.005 0.001 TYR B 289 ARG 0.001 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.600 Fit side-chains REVERT: A 234 TRP cc_start: 0.8362 (p90) cc_final: 0.8030 (p-90) REVERT: B 234 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: B 339 TRP cc_start: 0.8510 (m100) cc_final: 0.8070 (m-10) REVERT: G 41 CYS cc_start: 0.8192 (m) cc_final: 0.7754 (p) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.0960 time to fit residues: 11.6197 Evaluate side-chains 78 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5785 Z= 0.287 Angle : 0.517 9.603 7964 Z= 0.277 Chirality : 0.041 0.142 992 Planarity : 0.003 0.036 1040 Dihedral : 5.907 112.383 958 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.96 % Allowed : 17.68 % Favored : 78.35 % 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: 0.43 (0.29), residues: 870 helix: 2.27 (0.28), residues: 361 sheet: -0.93 (0.42), residues: 152 loop : -1.28 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 297 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE B 235 TYR 0.016 0.001 TYR A 360 ARG 0.004 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.710 Fit side-chains REVERT: A 234 TRP cc_start: 0.8490 (p90) cc_final: 0.8189 (p-90) REVERT: B 234 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: B 339 TRP cc_start: 0.8644 (m100) cc_final: 0.8028 (m-10) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.1083 time to fit residues: 11.6416 Evaluate side-chains 72 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.0020 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5785 Z= 0.152 Angle : 0.449 9.743 7964 Z= 0.236 Chirality : 0.039 0.127 992 Planarity : 0.003 0.033 1040 Dihedral : 5.630 109.401 958 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.96 % Allowed : 17.99 % Favored : 78.05 % 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: 0.65 (0.30), residues: 870 helix: 2.51 (0.29), residues: 355 sheet: -0.91 (0.42), residues: 152 loop : -1.11 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE B 292 TYR 0.008 0.001 TYR A 360 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.671 Fit side-chains REVERT: A 234 TRP cc_start: 0.8503 (p90) cc_final: 0.8196 (p-90) REVERT: B 234 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: B 339 TRP cc_start: 0.8592 (m100) cc_final: 0.8005 (m-10) REVERT: G 41 CYS cc_start: 0.8168 (m) cc_final: 0.7718 (p) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.0962 time to fit residues: 10.6783 Evaluate side-chains 71 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 57.7744 > 50: distance: 68 - 69: 4.685 distance: 69 - 70: 4.354 distance: 72 - 73: 3.213 distance: 73 - 74: 4.786 distance: 73 - 76: 4.523 distance: 74 - 75: 3.102 distance: 74 - 80: 4.791 distance: 76 - 77: 3.304 distance: 76 - 78: 3.989 distance: 77 - 79: 5.118 distance: 80 - 81: 5.222 distance: 81 - 82: 10.724 distance: 81 - 84: 6.313 distance: 82 - 83: 27.943 distance: 82 - 87: 32.942 distance: 84 - 85: 6.090 distance: 84 - 86: 13.577 distance: 87 - 88: 19.074 distance: 88 - 89: 13.949 distance: 88 - 91: 9.510 distance: 89 - 90: 3.718 distance: 89 - 93: 6.298 distance: 90 - 169: 5.232 distance: 91 - 92: 21.925 distance: 93 - 94: 11.482 distance: 94 - 95: 11.890 distance: 94 - 97: 3.074 distance: 95 - 96: 7.910 distance: 95 - 100: 7.186 distance: 97 - 98: 10.382 distance: 97 - 99: 9.361 distance: 100 - 101: 4.054 distance: 100 - 162: 5.763 distance: 101 - 102: 3.931 distance: 101 - 104: 3.119 distance: 102 - 103: 3.259 distance: 102 - 106: 3.798 distance: 103 - 159: 5.715 distance: 104 - 105: 6.740 distance: 106 - 107: 3.046 distance: 107 - 108: 5.243 distance: 108 - 109: 3.705 distance: 110 - 111: 3.708 distance: 111 - 112: 3.043 distance: 111 - 113: 5.856 distance: 112 - 114: 7.426 distance: 113 - 115: 4.278 distance: 114 - 116: 6.351 distance: 115 - 116: 8.092 distance: 117 - 118: 5.868 distance: 119 - 120: 4.141 distance: 119 - 123: 5.620 distance: 121 - 122: 4.322 distance: 124 - 125: 4.435 distance: 125 - 126: 3.973 distance: 125 - 132: 4.196 distance: 127 - 128: 10.327 distance: 128 - 129: 7.299 distance: 129 - 130: 6.970 distance: 130 - 131: 12.312 distance: 132 - 133: 6.495 distance: 133 - 136: 7.383 distance: 134 - 135: 5.346 distance: 136 - 137: 7.251