Starting phenix.real_space_refine on Tue Dec 12 16:31:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/12_2023/7bh1_12185_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/12_2023/7bh1_12185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/12_2023/7bh1_12185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/12_2023/7bh1_12185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/12_2023/7bh1_12185_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/12_2023/7bh1_12185_trim_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.088 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6977 2.51 5 N 1818 2.21 5 O 1964 1.98 5 H 11139 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 208": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 21961 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 10201 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2827 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 13, 'TRANS': 172} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 421 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.88, per 1000 atoms: 0.45 Number of scatterers: 21961 At special positions: 0 Unit cell: (78.66, 114.885, 157.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 61 16.00 P 1 15.00 O 1964 8.00 N 1818 7.00 C 6977 6.00 H 11139 1.00 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: 18.98 Conformation dependent library (CDL) restraints added in 2.6 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 6 sheets defined 57.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 41 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 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 Processing helix chain 'A' and resid 166 through 192 removed outlier: 4.180A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.408A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.501A pdb=" N MET A 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 298 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.749A pdb=" N LEU A 312 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.545A 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 398 Processing helix chain 'A' and resid 411 through 437 removed outlier: 3.784A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.359A 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 removed outlier: 3.685A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 507 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 525 through 548 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 62 through 101 removed outlier: 3.642A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 Processing helix chain 'B' and resid 216 through 246 removed outlier: 4.508A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 5.037A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 330 through 343 removed outlier: 4.574A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 520 through 528 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.648A pdb=" N ALA B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 594 removed outlier: 3.527A pdb=" N LEU B 569 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 585 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 587 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 4.050A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 630 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 646 through 679 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 21 through 33 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: 3.530A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.896A 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 162 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 3 through 23 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 Processing sheet with id= B, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.557A pdb=" N ASP B 119 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.653A pdb=" N VAL B 188 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 150 through 153 Processing sheet with id= E, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.485A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 383 through 386 removed outlier: 5.447A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS B 446 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA B 319 " --> pdb=" O LYS B 446 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1575 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: 8.43 Time building geometry restraints manager: 19.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11127 1.03 - 1.22: 106 1.22 - 1.42: 4295 1.42 - 1.62: 6513 1.62 - 1.81: 112 Bond restraints: 22153 Sorted by residual: bond pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 1.333 1.532 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" ND2 ASN B 582 " pdb="HD21 ASN B 582 " ideal model delta sigma weight residual 0.860 0.972 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" ND2 ASN B 582 " pdb="HD22 ASN B 582 " ideal model delta sigma weight residual 0.860 0.966 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C21 9Y0 B 801 " pdb=" O7 9Y0 B 801 " ideal model delta sigma weight residual 1.330 1.417 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 22148 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.20: 313 105.20 - 112.50: 26327 112.50 - 119.79: 6348 119.79 - 127.08: 7064 127.08 - 134.38: 135 Bond angle restraints: 40187 Sorted by residual: angle pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " pdb=" C15 9Y0 B 801 " ideal model delta sigma weight residual 127.64 104.93 22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" C12 9Y0 B 801 " pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 127.16 114.64 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O 9Y0 B 801 " pdb=" P 9Y0 B 801 " pdb=" O2 9Y0 B 801 " ideal model delta sigma weight residual 120.70 108.37 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C6 9Y0 B 801 " pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " ideal model delta sigma weight residual 111.26 122.17 -10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C2 9Y0 B 801 " pdb=" O3 9Y0 B 801 " pdb=" P 9Y0 B 801 " ideal model delta sigma weight residual 119.47 108.60 10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 40182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.35: 9645 27.35 - 54.71: 371 54.71 - 82.06: 42 82.06 - 109.42: 4 109.42 - 136.77: 1 Dihedral angle restraints: 10063 sinusoidal: 5403 harmonic: 4660 Sorted by residual: dihedral pdb=" CA LEU A 36 " pdb=" C LEU A 36 " pdb=" N PRO A 37 " pdb=" CA PRO A 37 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C 9Y0 B 801 " pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " pdb=" C6 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual 183.38 46.61 136.77 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 10060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1471 0.076 - 0.153: 300 0.153 - 0.229: 27 0.229 - 0.305: 3 0.305 - 0.382: 1 Chirality restraints: 1802 Sorted by residual: chirality pdb=" C1 9Y0 B 801 " pdb=" C 9Y0 B 801 " pdb=" C2 9Y0 B 801 " pdb=" O7 9Y0 B 801 " both_signs ideal model delta sigma weight residual False 2.36 2.74 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB ILE B 580 " pdb=" CA ILE B 580 " pdb=" CG1 ILE B 580 " pdb=" CG2 ILE B 580 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA PRO B 34 " pdb=" N PRO B 34 " pdb=" C PRO B 34 " pdb=" CB PRO B 34 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1799 not shown) Planarity restraints: 3275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 582 " -0.236 2.00e-02 2.50e+03 2.46e-01 9.06e+02 pdb=" CG ASN B 582 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B 582 " 0.224 2.00e-02 2.50e+03 pdb=" ND2 ASN B 582 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN B 582 " 0.352 2.00e-02 2.50e+03 pdb="HD22 ASN B 582 " -0.363 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.039 2.00e-02 2.50e+03 7.11e-02 7.58e+01 pdb=" CG ASN B 624 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " -0.124 2.00e-02 2.50e+03 pdb="HD21 ASN B 624 " -0.011 2.00e-02 2.50e+03 pdb="HD22 ASN B 624 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 B 801 " 0.045 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C13 9Y0 B 801 " -0.053 2.00e-02 2.50e+03 pdb=" C14 9Y0 B 801 " -0.035 2.00e-02 2.50e+03 pdb=" C15 9Y0 B 801 " 0.043 2.00e-02 2.50e+03 ... (remaining 3272 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.34: 7481 2.34 - 3.04: 65569 3.04 - 3.74: 82073 3.74 - 4.44: 129815 4.44 - 5.14: 200812 Nonbonded interactions: 485750 Sorted by model distance: nonbonded pdb=" OD1 ASN A 447 " pdb=" H ALA C 88 " model vdw 1.640 1.850 nonbonded pdb=" OD1 ASP B 335 " pdb="HE21 GLN B 338 " model vdw 1.660 1.850 nonbonded pdb=" HE ARG B 365 " pdb=" OG SER B 369 " model vdw 1.666 1.850 nonbonded pdb="HH11 ARG B 167 " pdb=" O PHE B 173 " model vdw 1.683 1.850 nonbonded pdb=" OD1 ASP B 550 " pdb=" H LEU B 551 " model vdw 1.692 1.850 ... (remaining 485745 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.360 Extract box with map and model: 8.190 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 78.560 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.014 0.199 11014 Z= 0.914 Angle : 1.148 22.705 14980 Z= 0.617 Chirality : 0.060 0.382 1802 Planarity : 0.007 0.075 1899 Dihedral : 14.321 136.773 3937 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.35 % Allowed : 11.32 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.18), residues: 1436 helix: -1.56 (0.15), residues: 852 sheet: -3.20 (0.48), residues: 67 loop : -3.44 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 32 HIS 0.008 0.002 HIS C 66 PHE 0.041 0.004 PHE A 260 TYR 0.046 0.004 TYR A 381 ARG 0.012 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.4433 time to fit residues: 85.6465 Evaluate side-chains 98 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.619 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2339 time to fit residues: 2.4468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN B 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11014 Z= 0.217 Angle : 0.612 6.678 14980 Z= 0.326 Chirality : 0.040 0.172 1802 Planarity : 0.005 0.052 1899 Dihedral : 9.307 86.559 1563 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.53 % Allowed : 13.44 % Favored : 86.03 % 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: -2.17 (0.20), residues: 1436 helix: -0.38 (0.16), residues: 852 sheet: -2.40 (0.46), residues: 84 loop : -3.11 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS A 451 PHE 0.021 0.002 PHE A 327 TYR 0.029 0.002 TYR A 381 ARG 0.002 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.4902 time to fit residues: 92.0321 Evaluate side-chains 104 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 2.001 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3907 time to fit residues: 5.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 50.3271 > 50: distance: 53 - 62: 7.085 distance: 62 - 63: 14.079 distance: 62 - 67: 12.653 distance: 63 - 64: 8.133 distance: 63 - 66: 5.244 distance: 63 - 68: 13.075 distance: 64 - 65: 19.539 distance: 64 - 72: 16.818 distance: 66 - 69: 4.608 distance: 66 - 71: 3.410 distance: 72 - 73: 10.743 distance: 72 - 76: 19.706 distance: 73 - 74: 3.664 distance: 73 - 77: 12.858 distance: 73 - 78: 26.781 distance: 74 - 75: 17.164 distance: 74 - 79: 6.397 distance: 79 - 80: 7.043 distance: 79 - 90: 5.999 distance: 80 - 91: 4.057 distance: 81 - 82: 6.385 distance: 81 - 103: 6.729 distance: 83 - 84: 4.307 distance: 83 - 92: 4.968 distance: 83 - 93: 5.861 distance: 84 - 85: 5.964 distance: 84 - 94: 4.721 distance: 84 - 95: 5.720 distance: 85 - 86: 4.600 distance: 85 - 96: 5.117 distance: 86 - 87: 3.945 distance: 86 - 98: 6.016 distance: 87 - 89: 3.480 distance: 88 - 99: 4.312 distance: 88 - 100: 3.877 distance: 89 - 102: 3.181 distance: 103 - 104: 8.924 distance: 103 - 109: 9.786 distance: 104 - 107: 6.181 distance: 104 - 110: 3.478 distance: 105 - 106: 3.838 distance: 105 - 114: 6.136 distance: 107 - 108: 6.297 distance: 107 - 111: 4.681 distance: 107 - 112: 11.362 distance: 108 - 113: 7.003 distance: 114 - 115: 3.479 distance: 114 - 119: 9.429 distance: 115 - 116: 4.974 distance: 115 - 118: 18.923 distance: 115 - 120: 9.219 distance: 116 - 117: 8.539 distance: 116 - 124: 10.866 distance: 118 - 121: 20.015 distance: 118 - 122: 11.954 distance: 118 - 123: 16.110 distance: 124 - 125: 10.081 distance: 124 - 132: 6.822 distance: 125 - 126: 4.354 distance: 125 - 128: 5.949 distance: 126 - 127: 6.965 distance: 126 - 141: 3.721 distance: 128 - 129: 6.881 distance: 128 - 134: 18.155 distance: 128 - 135: 8.115 distance: 129 - 130: 8.378 distance: 129 - 136: 3.779 distance: 129 - 137: 5.926 distance: 130 - 131: 11.202 distance: 131 - 138: 4.900 distance: 131 - 139: 4.533 distance: 141 - 149: 10.897 distance: 142 - 143: 11.865 distance: 142 - 145: 9.372 distance: 142 - 150: 11.659 distance: 143 - 144: 14.936 distance: 143 - 160: 8.200 distance: 145 - 146: 4.662 distance: 145 - 151: 6.257 distance: 145 - 152: 8.531 distance: 146 - 147: 4.053 distance: 146 - 153: 8.946 distance: 147 - 154: 4.492 distance: 147 - 155: 8.467 distance: 147 - 156: 8.790 distance: 148 - 157: 4.310 distance: 148 - 158: 5.710 distance: 148 - 159: 6.614 distance: 160 - 161: 7.935 distance: 160 - 168: 13.703 distance: 161 - 162: 8.053 distance: 161 - 164: 8.426 distance: 161 - 169: 12.787 distance: 162 - 163: 24.304 distance: 162 - 174: 4.792 distance: 164 - 165: 3.972 distance: 164 - 170: 4.822 distance: 164 - 171: 8.705 distance: 165 - 166: 9.777 distance: 165 - 167: 3.384 distance: 167 - 172: 3.177 distance: 167 - 173: 8.102 distance: 174 - 175: 16.970 distance: 174 - 180: 8.494 distance: 175 - 176: 15.759 distance: 175 - 178: 11.060 distance: 175 - 181: 19.598 distance: 176 - 177: 8.860 distance: 176 - 188: 6.451 distance: 178 - 179: 5.865 distance: 178 - 182: 4.362 distance: 178 - 183: 5.278 distance: 179 - 180: 10.122 distance: 179 - 184: 11.189 distance: 179 - 185: 6.884 distance: 180 - 186: 22.542 distance: 180 - 187: 13.367 distance: 188 - 189: 8.914 distance: 189 - 190: 11.611 distance: 189 - 193: 4.159 distance: 189 - 194: 6.698 distance: 190 - 191: 8.592 distance: 190 - 195: 8.554 distance: 191 - 229: 8.515