Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 3 08:18:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/05_2023/7lwd_23545_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/05_2023/7lwd_23545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/05_2023/7lwd_23545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/05_2023/7lwd_23545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/05_2023/7lwd_23545_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/05_2023/7lwd_23545_updated.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 129 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4067 2.51 5 N 975 2.21 5 O 1087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A GLU 606": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 6163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4319 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 517} Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 101 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 37 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C08AYG7 A 802 " occ=0.50 ... (64 atoms not shown) pdb=" O02BYG7 A 802 " occ=0.50 Time building chain proxies: 4.05, per 1000 atoms: 0.66 Number of scatterers: 6163 At special positions: 0 Unit cell: (84.888, 73.872, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1087 8.00 N 975 7.00 C 4067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 5 sheets defined 45.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.711A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 removed outlier: 5.212A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.737A pdb=" N GLN A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.745A pdb=" N MET A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 156 through 188 removed outlier: 4.179A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.855A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.762A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.174A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 361 through 389 removed outlier: 4.303A pdb=" N SER A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 425 through 453 removed outlier: 3.844A pdb=" N GLY A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 485 through 495 removed outlier: 4.831A pdb=" N LYS A 490 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 495 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.972A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.483A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.539A pdb=" N LEU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.810A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 4.137A pdb=" N SER A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 83 through 86 No H-bonds generated for 'chain 'H' and resid 83 through 86' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing sheet with id= A, first strand: chain 'H' and resid 38 through 42 removed outlier: 3.648A pdb=" N ILE H 39 " --> pdb=" O MET H 100 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 88 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 56 through 58 removed outlier: 3.709A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 24 through 27 removed outlier: 3.545A pdb=" N SER L 27 " --> pdb=" O SER L 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 112 through 114 removed outlier: 3.593A pdb=" N TRP L 59 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE L 72 " --> pdb=" O TRP L 59 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN L 61 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU L 70 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 89 through 91 removed outlier: 4.148A pdb=" N TYR L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 926 1.25 - 1.39: 1706 1.39 - 1.53: 3326 1.53 - 1.67: 346 1.67 - 1.81: 49 Bond restraints: 6353 Sorted by residual: bond pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 1.351 1.588 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 1.351 1.587 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C21BYG7 A 802 " pdb=" C26BYG7 A 802 " ideal model delta sigma weight residual 1.432 1.224 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C21AYG7 A 802 " pdb=" C26AYG7 A 802 " ideal model delta sigma weight residual 1.432 1.226 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 1.354 1.171 0.183 2.00e-02 2.50e+03 8.38e+01 ... (remaining 6348 not shown) Histogram of bond angle deviations from ideal: 88.85 - 107.07: 188 107.07 - 125.30: 8309 125.30 - 143.53: 154 143.53 - 161.75: 0 161.75 - 179.98: 2 Bond angle restraints: 8653 Sorted by residual: angle pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 111.69 131.58 -19.89 3.00e+00 1.11e-01 4.39e+01 angle pdb=" C26AYG7 A 802 " pdb=" C29AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 111.69 131.49 -19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 106.53 88.85 17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " pdb=" C29AYG7 A 802 " ideal model delta sigma weight residual 106.53 88.98 17.55 3.00e+00 1.11e-01 3.42e+01 angle pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta sigma weight residual 121.70 131.48 -9.78 1.80e+00 3.09e-01 2.95e+01 ... (remaining 8648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 3520 33.23 - 66.46: 67 66.46 - 99.69: 6 99.69 - 132.92: 2 132.92 - 166.15: 2 Dihedral angle restraints: 3597 sinusoidal: 1387 harmonic: 2210 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 142.29 -49.29 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" C13BYG7 A 802 " pdb=" C14BYG7 A 802 " pdb=" C16BYG7 A 802 " pdb=" C17BYG7 A 802 " ideal model delta sinusoidal sigma weight residual -62.61 103.54 -166.15 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 22.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 546 0.031 - 0.061: 283 0.061 - 0.092: 78 0.092 - 0.122: 30 0.122 - 0.153: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA PHE A 380 " pdb=" N PHE A 380 " pdb=" C PHE A 380 " pdb=" CB PHE A 380 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE L 41 " pdb=" N ILE L 41 " pdb=" C ILE L 41 " pdb=" CB ILE L 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA TRP A 103 " pdb=" N TRP A 103 " pdb=" C TRP A 103 " pdb=" CB TRP A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 935 not shown) Planarity restraints: 1060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C PHE A 465 " -0.048 2.00e-02 2.50e+03 pdb=" O PHE A 465 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 466 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 103 " 0.014 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP A 103 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 103 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 103 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 288 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.020 5.00e-02 4.00e+02 ... (remaining 1057 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 52 2.60 - 3.17: 5570 3.17 - 3.75: 9646 3.75 - 4.32: 13542 4.32 - 4.90: 22119 Nonbonded interactions: 50929 Sorted by model distance: nonbonded pdb=" ND2 ASN A 208 " pdb=" C1 NAG A 803 " model vdw 2.024 3.550 nonbonded pdb=" OG SER A 199 " pdb=" OD2 ASP H 74 " model vdw 2.209 2.440 nonbonded pdb=" ND2 ASN A 208 " pdb=" C2 NAG A 803 " model vdw 2.225 3.550 nonbonded pdb=" OH TYR A 185 " pdb=" OE1 GLN A 254 " model vdw 2.319 2.440 nonbonded pdb=" NE2 GLN H 25 " pdb=" OG1 THR H 134 " model vdw 2.326 2.520 ... (remaining 50924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 13.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.011 0.237 6353 Z= 0.672 Angle : 0.972 19.885 8653 Z= 0.406 Chirality : 0.039 0.153 938 Planarity : 0.004 0.036 1060 Dihedral : 14.882 166.146 2186 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -4.15 (0.25), residues: 763 helix: -1.97 (0.23), residues: 353 sheet: -4.04 (0.39), residues: 93 loop : -3.15 (0.30), residues: 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1821 time to fit residues: 31.1257 Evaluate side-chains 105 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 177 ASN A 208 ASN A 368 ASN A 416 ASN H 25 GLN L 62 GLN L 78 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6353 Z= 0.235 Angle : 0.569 9.593 8653 Z= 0.295 Chirality : 0.041 0.158 938 Planarity : 0.005 0.047 1060 Dihedral : 10.678 171.121 869 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -3.15 (0.28), residues: 763 helix: -1.18 (0.26), residues: 352 sheet: -3.55 (0.44), residues: 90 loop : -2.58 (0.33), residues: 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.1632 time to fit residues: 25.3471 Evaluate side-chains 108 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0616 time to fit residues: 1.7629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6353 Z= 0.229 Angle : 0.552 9.556 8653 Z= 0.288 Chirality : 0.041 0.165 938 Planarity : 0.004 0.040 1060 Dihedral : 10.621 168.171 869 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.81 (0.29), residues: 763 helix: -0.96 (0.26), residues: 353 sheet: -3.27 (0.47), residues: 90 loop : -2.38 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.701 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 0.1567 time to fit residues: 25.2080 Evaluate side-chains 103 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0602 time to fit residues: 1.4339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6353 Z= 0.195 Angle : 0.525 9.493 8653 Z= 0.275 Chirality : 0.040 0.155 938 Planarity : 0.004 0.039 1060 Dihedral : 10.509 167.323 869 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.54 (0.29), residues: 763 helix: -0.75 (0.27), residues: 355 sheet: -3.03 (0.48), residues: 90 loop : -2.26 (0.34), residues: 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.638 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 106 average time/residue: 0.1634 time to fit residues: 23.9693 Evaluate side-chains 100 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0631 time to fit residues: 1.2987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6353 Z= 0.205 Angle : 0.536 9.492 8653 Z= 0.280 Chirality : 0.040 0.157 938 Planarity : 0.004 0.038 1060 Dihedral : 10.407 165.719 869 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.47 (0.29), residues: 763 helix: -0.76 (0.27), residues: 362 sheet: -3.11 (0.50), residues: 79 loop : -2.18 (0.34), residues: 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.1624 time to fit residues: 24.2097 Evaluate side-chains 106 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0651 time to fit residues: 2.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 70 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6353 Z= 0.181 Angle : 0.533 9.527 8653 Z= 0.277 Chirality : 0.039 0.165 938 Planarity : 0.004 0.038 1060 Dihedral : 10.401 165.613 869 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.20 (0.30), residues: 763 helix: -0.58 (0.27), residues: 357 sheet: -2.69 (0.50), residues: 89 loop : -2.02 (0.35), residues: 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 106 average time/residue: 0.1524 time to fit residues: 22.7626 Evaluate side-chains 98 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0710 time to fit residues: 1.6242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 50.836 > 50: distance: 71 - 77: 3.312 distance: 77 - 78: 4.144 distance: 78 - 79: 9.615 distance: 78 - 81: 4.464 distance: 79 - 80: 6.901 distance: 79 - 87: 7.088 distance: 81 - 82: 4.387 distance: 82 - 83: 4.138 distance: 82 - 84: 4.830 distance: 83 - 85: 3.990 distance: 84 - 86: 4.260 distance: 85 - 86: 3.393 distance: 87 - 88: 3.881 distance: 87 - 93: 7.307 distance: 88 - 89: 7.575 distance: 88 - 91: 8.930 distance: 89 - 90: 22.893 distance: 89 - 94: 3.114 distance: 91 - 92: 5.960 distance: 92 - 93: 12.550 distance: 94 - 95: 4.468 distance: 95 - 96: 5.480 distance: 95 - 98: 9.819 distance: 96 - 97: 20.231 distance: 96 - 102: 7.424 distance: 98 - 99: 8.425 distance: 99 - 100: 8.987 distance: 100 - 101: 7.198 distance: 102 - 103: 6.625 distance: 103 - 104: 5.507 distance: 103 - 106: 12.330 distance: 104 - 105: 27.929 distance: 104 - 111: 25.106 distance: 106 - 107: 4.883 distance: 108 - 109: 3.296 distance: 111 - 112: 7.987 distance: 112 - 113: 15.375 distance: 112 - 115: 14.806 distance: 113 - 114: 37.885 distance: 113 - 120: 10.283 distance: 115 - 116: 10.502 distance: 116 - 117: 17.829 distance: 117 - 118: 4.649 distance: 117 - 119: 4.010 distance: 120 - 121: 6.501 distance: 121 - 122: 11.009 distance: 121 - 124: 13.474 distance: 122 - 123: 16.041 distance: 122 - 128: 14.478 distance: 124 - 125: 16.485 distance: 125 - 126: 13.302 distance: 125 - 127: 16.201 distance: 128 - 129: 13.755 distance: 129 - 130: 9.779 distance: 129 - 132: 15.863 distance: 130 - 131: 19.040 distance: 130 - 136: 19.618 distance: 132 - 133: 11.302 distance: 133 - 134: 11.188 distance: 133 - 135: 7.210 distance: 136 - 137: 14.311 distance: 137 - 138: 13.874 distance: 137 - 140: 16.701 distance: 138 - 139: 11.575 distance: 138 - 143: 10.603 distance: 140 - 141: 6.520 distance: 140 - 142: 3.644 distance: 143 - 144: 15.628 distance: 144 - 145: 15.776 distance: 144 - 147: 9.854 distance: 145 - 146: 13.553 distance: 145 - 148: 15.874 distance: 149 - 150: 8.787 distance: 149 - 152: 3.512 distance: 150 - 151: 12.990 distance: 150 - 155: 5.363 distance: 152 - 153: 9.657