Starting phenix.real_space_refine on Sat Dec 9 13:09:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnl_12478/12_2023/7nnl_12478_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnl_12478/12_2023/7nnl_12478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnl_12478/12_2023/7nnl_12478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnl_12478/12_2023/7nnl_12478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnl_12478/12_2023/7nnl_12478_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnl_12478/12_2023/7nnl_12478_updated.pdb" } resolution = 3.1 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= 0.008 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 K 10 8.98 5 P 8 5.49 5 S 63 5.16 5 C 7165 2.51 5 N 1838 2.21 5 O 2015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 473": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11099 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5072 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 26, 'TRANS': 655} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Unusual residues: {' K': 8, 'CDL': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 2, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.37, per 1000 atoms: 0.57 Number of scatterers: 11099 At special positions: 0 Unit cell: (97.152, 115.368, 145.728, 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) K 10 19.00 S 63 16.00 P 8 15.00 O 2015 8.00 N 1838 7.00 C 7165 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: 4.72 Conformation dependent library (CDL) restraints added in 1.9 seconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 6 sheets defined 55.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 removed outlier: 3.842A pdb=" N ARG A 21 " --> pdb=" O MET A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.619A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.692A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 135 through 156 removed outlier: 3.582A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 179 through 192 removed outlier: 3.889A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.802A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.521A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.520A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.794A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.850A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.686A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 383 through 398 Processing helix chain 'A' and resid 411 through 437 removed outlier: 4.627A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 524 through 548 removed outlier: 3.790A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 148 removed outlier: 3.994A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 removed outlier: 3.822A pdb=" N GLY D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 removed outlier: 3.658A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 62 through 98 removed outlier: 3.769A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 245 removed outlier: 3.915A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.991A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 284 removed outlier: 3.616A pdb=" N LEU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.768A pdb=" N ALA B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 4.316A pdb=" N ALA B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 347 through 355 Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.798A pdb=" N GLN B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 520 through 526 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 558 through 594 removed outlier: 3.702A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.687A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.095A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 removed outlier: 4.167A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.627A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= E, first strand: chain 'B' and resid 489 through 491 removed outlier: 3.617A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 306 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 512 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 304 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA B 514 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU B 306 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR B 516 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 531 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY B 517 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 533 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 393 through 396 removed outlier: 6.117A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1518 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: 3.14 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1781 1.31 - 1.44: 2759 1.44 - 1.57: 6618 1.57 - 1.69: 15 1.69 - 1.82: 116 Bond restraints: 11289 Sorted by residual: bond pdb=" CB7 CDL A 610 " pdb=" OB8 CDL A 610 " ideal model delta sigma weight residual 1.334 1.424 -0.090 1.10e-02 8.26e+03 6.76e+01 bond pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.421 -0.087 1.10e-02 8.26e+03 6.23e+01 bond pdb=" CA7 CDL A 610 " pdb=" OA8 CDL A 610 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" CA7 CDL A 609 " pdb=" OA8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" OB2 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.579 1.667 -0.088 1.50e-02 4.44e+03 3.42e+01 ... (remaining 11284 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.44: 254 105.44 - 112.61: 6112 112.61 - 119.77: 3691 119.77 - 126.94: 5133 126.94 - 134.11: 132 Bond angle restraints: 15322 Sorted by residual: angle pdb=" C51 CDL A 609 " pdb=" CB5 CDL A 609 " pdb=" OB6 CDL A 609 " ideal model delta sigma weight residual 111.33 120.17 -8.84 1.32e+00 5.72e-01 4.47e+01 angle pdb=" C11 CDL A 610 " pdb=" CA5 CDL A 610 " pdb=" OA6 CDL A 610 " ideal model delta sigma weight residual 111.33 119.96 -8.63 1.32e+00 5.72e-01 4.26e+01 angle pdb=" C11 CDL A 609 " pdb=" CA5 CDL A 609 " pdb=" OA6 CDL A 609 " ideal model delta sigma weight residual 111.33 119.79 -8.46 1.32e+00 5.72e-01 4.09e+01 angle pdb=" C51 CDL A 610 " pdb=" CB5 CDL A 610 " pdb=" OB6 CDL A 610 " ideal model delta sigma weight residual 111.33 119.45 -8.12 1.32e+00 5.72e-01 3.78e+01 angle pdb=" C71 CDL A 610 " pdb=" CB7 CDL A 610 " pdb=" OB8 CDL A 610 " ideal model delta sigma weight residual 111.64 120.94 -9.30 1.65e+00 3.69e-01 3.19e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.67: 6274 22.67 - 45.34: 408 45.34 - 68.00: 99 68.00 - 90.67: 21 90.67 - 113.34: 1 Dihedral angle restraints: 6803 sinusoidal: 2679 harmonic: 4124 Sorted by residual: dihedral pdb=" CA GLN B 28 " pdb=" C GLN B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA MET A 397 " pdb=" C MET A 397 " pdb=" N ILE A 398 " pdb=" CA ILE A 398 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 6800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1477 0.059 - 0.117: 312 0.117 - 0.175: 29 0.175 - 0.234: 3 0.234 - 0.292: 1 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1819 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 496 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 262 " 0.038 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 263 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 471 " -0.019 2.00e-02 2.50e+03 1.62e-02 4.60e+00 pdb=" CG PHE A 471 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 471 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 471 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 471 " -0.004 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3038 2.81 - 3.39: 12461 3.39 - 3.98: 22000 3.98 - 4.56: 31402 4.56 - 5.14: 45664 Nonbonded interactions: 114565 Sorted by model distance: nonbonded pdb=" OG SER B 90 " pdb=" O VAL B 207 " model vdw 2.230 2.440 nonbonded pdb=" OE2 GLU A 321 " pdb=" OG SER C 85 " model vdw 2.249 2.440 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR B 47 " pdb=" OG SER B 69 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR A 401 " pdb=" OD2 ASP B 300 " model vdw 2.300 2.440 ... (remaining 114560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 3.700 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.490 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 0.090 11289 Z= 0.369 Angle : 0.909 15.629 15322 Z= 0.474 Chirality : 0.046 0.292 1822 Planarity : 0.006 0.063 1918 Dihedral : 16.458 113.340 4153 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1445 helix: -0.08 (0.17), residues: 855 sheet: -1.21 (0.58), residues: 79 loop : -1.53 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 245 HIS 0.001 0.000 HIS A 451 PHE 0.037 0.002 PHE A 471 TYR 0.028 0.001 TYR A 381 ARG 0.017 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2218 time to fit residues: 45.4997 Evaluate side-chains 123 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.9248 > 50: distance: 41 - 48: 8.909 distance: 48 - 49: 17.753 distance: 49 - 50: 5.462 distance: 49 - 52: 13.705 distance: 50 - 51: 28.536 distance: 50 - 59: 17.179 distance: 52 - 53: 7.091 distance: 53 - 54: 5.781 distance: 53 - 55: 6.146 distance: 54 - 56: 5.419 distance: 55 - 57: 6.184 distance: 57 - 58: 3.792 distance: 59 - 60: 14.233 distance: 60 - 61: 4.664 distance: 60 - 63: 11.635 distance: 61 - 62: 32.219 distance: 61 - 67: 27.281 distance: 64 - 65: 9.521 distance: 64 - 66: 8.842 distance: 67 - 68: 8.733 distance: 68 - 69: 16.617 distance: 68 - 71: 14.880 distance: 69 - 70: 46.620 distance: 69 - 75: 32.923 distance: 71 - 72: 17.201 distance: 72 - 73: 16.516 distance: 72 - 74: 22.054 distance: 75 - 76: 14.492 distance: 76 - 77: 12.718 distance: 76 - 79: 33.353 distance: 77 - 78: 31.814 distance: 77 - 86: 18.803 distance: 79 - 80: 4.259 distance: 80 - 81: 10.782 distance: 82 - 83: 3.177 distance: 86 - 87: 8.941 distance: 87 - 88: 10.792 distance: 87 - 90: 26.435 distance: 88 - 89: 10.202 distance: 88 - 95: 14.187 distance: 90 - 91: 13.681 distance: 91 - 92: 8.261 distance: 92 - 93: 4.383 distance: 92 - 94: 5.228 distance: 95 - 96: 7.106 distance: 96 - 97: 18.220 distance: 96 - 99: 17.372 distance: 97 - 98: 27.767 distance: 97 - 106: 25.986 distance: 99 - 100: 7.845 distance: 100 - 101: 4.772 distance: 106 - 107: 24.485 distance: 107 - 108: 12.853 distance: 107 - 110: 5.846 distance: 108 - 109: 36.323 distance: 108 - 114: 22.676 distance: 110 - 111: 25.403 distance: 111 - 112: 13.130 distance: 111 - 113: 8.841 distance: 114 - 115: 24.180 distance: 115 - 116: 39.249 distance: 115 - 118: 40.653 distance: 116 - 117: 34.610 distance: 116 - 121: 20.995 distance: 118 - 119: 50.618 distance: 118 - 120: 44.782 distance: 121 - 122: 29.660 distance: 122 - 123: 48.075 distance: 122 - 125: 31.630 distance: 123 - 124: 51.707 distance: 123 - 130: 32.626 distance: 125 - 126: 9.299 distance: 126 - 127: 13.492 distance: 127 - 129: 4.840 distance: 130 - 131: 26.919 distance: 131 - 132: 12.314 distance: 131 - 134: 39.474 distance: 132 - 133: 40.099 distance: 132 - 136: 16.099 distance: 134 - 135: 49.437