Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 06:12:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/10_2023/7oto_13063_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/10_2023/7oto_13063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/10_2023/7oto_13063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/10_2023/7oto_13063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/10_2023/7oto_13063_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/10_2023/7oto_13063_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.023 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 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6472 2.51 5 N 1841 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ARG 697": "NH1" <-> "NH2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 697": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10333 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4697 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 25, 'TRANS': 576} Chain breaks: 1 Chain: "A" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5572 Classifications: {'peptide': 711} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain breaks: 3 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.78, per 1000 atoms: 0.56 Number of scatterers: 10333 At special positions: 0 Unit cell: (112.36, 121.9, 97.52, 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 51 16.00 P 6 15.00 Mg 2 11.99 O 1961 8.00 N 1841 7.00 C 6472 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: 4.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 10 sheets defined 48.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 231 through 247 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 335 through 345 Proline residue: B 340 - end of helix Processing helix chain 'B' and resid 349 through 356 Processing helix chain 'B' and resid 362 through 384 Proline residue: B 376 - end of helix removed outlier: 3.811A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 512 through 565 Proline residue: B 537 - end of helix removed outlier: 4.772A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ALA B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 4.078A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 636 Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 701 through 717 Processing helix chain 'B' and resid 732 through 738 Proline residue: B 736 - end of helix Processing helix chain 'B' and resid 772 through 779 Processing helix chain 'B' and resid 783 through 798 Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.516A pdb=" N ALA A 47 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 4.985A pdb=" N GLU A 77 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 231 through 248 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 335 through 345 Proline residue: A 340 - end of helix removed outlier: 3.532A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 362 through 384 Proline residue: A 376 - end of helix removed outlier: 3.525A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 513 through 565 Proline residue: A 537 - end of helix removed outlier: 4.953A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.808A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 636 removed outlier: 3.588A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 701 through 717 Processing helix chain 'A' and resid 730 through 738 Proline residue: A 736 - end of helix Processing helix chain 'A' and resid 772 through 779 Processing helix chain 'A' and resid 783 through 799 Processing sheet with id= A, first strand: chain 'B' and resid 132 through 138 removed outlier: 3.504A pdb=" N ARG B 154 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 178 through 181 Processing sheet with id= C, first strand: chain 'B' and resid 570 through 572 removed outlier: 6.683A pdb=" N VAL B 645 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 762 through 764 removed outlier: 6.462A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 723 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 612 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE B 725 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 749 through 751 Processing sheet with id= F, first strand: chain 'A' and resid 55 through 58 removed outlier: 5.224A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 112 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.325A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 601 through 603 removed outlier: 3.565A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 762 through 764 removed outlier: 6.316A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 723 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 612 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 725 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 749 through 752 498 hydrogen bonds defined for protein. 1398 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: 3.29 Time building geometry restraints manager: 4.54 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: 1765 1.31 - 1.44: 2562 1.44 - 1.57: 6071 1.57 - 1.69: 10 1.69 - 1.82: 91 Bond restraints: 10499 Sorted by residual: bond pdb=" N3B ANP A1002 " pdb=" PG ANP A1002 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" N3B ANP B1002 " pdb=" PG ANP B1002 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" O3A ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sigma weight residual 1.700 1.596 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O3A ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sigma weight residual 1.700 1.600 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ILE A 66 " pdb=" CA ILE A 66 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.07e+01 ... (remaining 10494 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.08: 348 106.08 - 113.14: 5052 113.14 - 120.20: 5078 120.20 - 127.26: 3683 127.26 - 134.32: 66 Bond angle restraints: 14227 Sorted by residual: angle pdb=" CA GLY B 422 " pdb=" C GLY B 422 " pdb=" O GLY B 422 " ideal model delta sigma weight residual 122.45 117.11 5.34 7.20e-01 1.93e+00 5.50e+01 angle pdb=" CA PHE A 725 " pdb=" CB PHE A 725 " pdb=" CG PHE A 725 " ideal model delta sigma weight residual 113.80 120.50 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" N PRO A 25 " pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 113.40 121.99 -8.59 1.34e+00 5.57e-01 4.11e+01 angle pdb=" CA SER B 604 " pdb=" C SER B 604 " pdb=" N PRO B 605 " ideal model delta sigma weight residual 117.68 122.22 -4.54 7.10e-01 1.98e+00 4.09e+01 angle pdb=" C PRO B 231 " pdb=" CA PRO B 231 " pdb=" CB PRO B 231 " ideal model delta sigma weight residual 113.06 102.93 10.13 1.59e+00 3.96e-01 4.06e+01 ... (remaining 14222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.08: 6228 32.08 - 64.17: 166 64.17 - 96.25: 23 96.25 - 128.34: 1 128.34 - 160.42: 1 Dihedral angle restraints: 6419 sinusoidal: 2620 harmonic: 3799 Sorted by residual: dihedral pdb=" O1A ANP B1002 " pdb=" O3A ANP B1002 " pdb=" PA ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sinusoidal sigma weight residual 83.11 -77.31 160.42 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A ANP A1002 " pdb=" O3A ANP A1002 " pdb=" PA ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sinusoidal sigma weight residual 83.11 -39.51 122.62 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C GLN B 248 " pdb=" N GLN B 248 " pdb=" CA GLN B 248 " pdb=" CB GLN B 248 " ideal model delta harmonic sigma weight residual -122.60 -113.29 -9.31 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 6416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 805 0.075 - 0.149: 540 0.149 - 0.224: 215 0.224 - 0.299: 68 0.299 - 0.373: 2 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C3' ANP A1002 " pdb=" C2' ANP A1002 " pdb=" C4' ANP A1002 " pdb=" O3' ANP A1002 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1627 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 268 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C ILE B 268 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 268 " 0.017 2.00e-02 2.50e+03 pdb=" N MET B 269 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 675 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C THR B 675 " 0.041 2.00e-02 2.50e+03 pdb=" O THR B 675 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 676 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 213 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C LEU B 213 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 213 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 214 " -0.014 2.00e-02 2.50e+03 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 4 2.42 - 3.04: 5563 3.04 - 3.66: 16012 3.66 - 4.28: 23125 4.28 - 4.90: 39236 Nonbonded interactions: 83940 Sorted by model distance: nonbonded pdb=" OG SER A 621 " pdb="MG MG A1001 " model vdw 1.799 2.170 nonbonded pdb=" OG SER B 621 " pdb="MG MG B1001 " model vdw 2.036 2.170 nonbonded pdb="MG MG A1001 " pdb=" O2B ANP A1002 " model vdw 2.128 2.170 nonbonded pdb="MG MG B1001 " pdb=" O1G ANP B1002 " model vdw 2.273 2.170 nonbonded pdb=" N ASP A 139 " pdb=" O ASP A 139 " model vdw 2.439 2.496 ... (remaining 83935 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: 0.010 Normalize map: mean=0, sd=1: 0.060 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: 0.980 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.760 Find NCS groups from input model: 0.270 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.013 0.175 10499 Z= 0.851 Angle : 1.836 14.147 14227 Z= 1.411 Chirality : 0.110 0.373 1630 Planarity : 0.006 0.034 1852 Dihedral : 15.173 160.421 3961 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.21), residues: 1301 helix: 3.35 (0.17), residues: 662 sheet: 0.72 (0.39), residues: 159 loop : -0.34 (0.24), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.3325 time to fit residues: 152.9327 Evaluate side-chains 280 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5432 ------------------------------------------------------------------------------- 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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 52.5284 > 50: distance: 55 - 56: 4.458 distance: 56 - 57: 3.803 distance: 56 - 59: 3.386 distance: 58 - 87: 6.935 distance: 62 - 63: 7.179 distance: 63 - 64: 6.114 distance: 64 - 65: 18.658 distance: 64 - 69: 21.844 distance: 66 - 67: 18.988 distance: 66 - 68: 36.927 distance: 69 - 70: 3.959 distance: 70 - 71: 8.950 distance: 70 - 73: 6.047 distance: 71 - 78: 6.600 distance: 73 - 74: 10.050 distance: 74 - 75: 7.878 distance: 75 - 77: 7.702 distance: 78 - 79: 6.164 distance: 79 - 80: 6.444 distance: 79 - 82: 3.161 distance: 82 - 83: 5.728 distance: 83 - 84: 9.696 distance: 84 - 85: 5.399 distance: 84 - 86: 6.866 distance: 87 - 88: 4.447 distance: 88 - 89: 4.604 distance: 89 - 90: 4.400 distance: 89 - 94: 3.010 distance: 91 - 92: 4.034 distance: 91 - 93: 3.065 distance: 95 - 98: 5.112 distance: 96 - 102: 6.197 distance: 98 - 99: 4.721 distance: 99 - 100: 3.166 distance: 99 - 101: 6.288 distance: 103 - 104: 3.798 distance: 103 - 106: 3.186 distance: 104 - 105: 7.595 distance: 104 - 110: 4.306 distance: 106 - 107: 3.876 distance: 107 - 108: 3.469 distance: 111 - 114: 3.511 distance: 112 - 113: 3.628 distance: 114 - 115: 7.836 distance: 115 - 116: 4.770 distance: 116 - 118: 6.459 distance: 119 - 120: 3.950 distance: 119 - 125: 8.833 distance: 120 - 123: 3.370 distance: 121 - 122: 5.045 distance: 123 - 124: 12.042 distance: 124 - 125: 6.988 distance: 127 - 130: 3.099 distance: 128 - 129: 6.014 distance: 130 - 131: 4.377 distance: 131 - 132: 8.146 distance: 131 - 133: 10.362 distance: 132 - 134: 3.632 distance: 133 - 135: 4.429 distance: 134 - 136: 12.008 distance: 135 - 136: 7.453