Starting phenix.real_space_refine on Thu Jan 18 22:57:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/01_2024/8p2s_17373_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/01_2024/8p2s_17373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/01_2024/8p2s_17373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/01_2024/8p2s_17373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/01_2024/8p2s_17373_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/01_2024/8p2s_17373_updated.pdb" } resolution = 2.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 Zn 1 6.06 5 P 9 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 6082 2.51 5 N 1687 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4417 Classifications: {'peptide': 550} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 529} Chain breaks: 1 Chain: "B" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5184 Classifications: {'peptide': 651} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 629} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' MG': 1, ' ZN': 1, 'GTP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9173 SG CYS B 680 14.461 51.845 61.872 1.00 63.96 S ATOM 9195 SG CYS B 683 13.936 55.137 59.924 1.00 64.44 S ATOM 9286 SG CYS B 695 12.496 54.640 63.508 1.00 71.47 S ATOM 9308 SG CYS B 698 11.067 52.943 60.445 1.00 72.94 S Time building chain proxies: 5.33, per 1000 atoms: 0.55 Number of scatterers: 9694 At special positions: 0 Unit cell: (77.456, 105.472, 115.36, 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) Zn 1 29.99 S 60 16.00 P 9 15.00 Mg 2 11.99 O 1853 8.00 N 1687 7.00 C 6082 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: 4.23 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 698 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 695 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 680 " Number of angles added : 6 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 9 sheets defined 45.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 122 through 138 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 230 through 247 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 273 through 301 Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 443 through 452 removed outlier: 4.533A pdb=" N GLY A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 487 removed outlier: 4.043A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.916A pdb=" N ILE A 517 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 545 through 569 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.889A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 634 Proline residue: A 630 - end of helix removed outlier: 4.234A pdb=" N ASP A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'B' and resid 86 through 104 removed outlier: 3.596A pdb=" N VAL B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 141 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'B' and resid 197 through 214 Processing helix chain 'B' and resid 224 through 247 Proline residue: B 230 - end of helix removed outlier: 3.599A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) 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 273 through 301 removed outlier: 3.739A pdb=" N ASN B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.655A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 456 through 486 Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 514 through 519 removed outlier: 4.369A pdb=" N ASN B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 514 through 519' Processing helix chain 'B' and resid 545 through 569 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 621 through 634 Proline residue: B 630 - end of helix removed outlier: 4.258A pdb=" N ASP B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 651 removed outlier: 4.000A pdb=" N HIS B 651 " --> pdb=" O GLY B 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 647 through 651' Processing helix chain 'B' and resid 654 through 665 Processing helix chain 'B' and resid 717 through 719 No H-bonds generated for 'chain 'B' and resid 717 through 719' Processing helix chain 'B' and resid 722 through 729 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 158 removed outlier: 7.278A pdb=" N THR A 521 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE A 438 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 523 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR A 440 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLY A 525 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASN A 442 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE A 527 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 184 through 186 Processing sheet with id= C, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.353A pdb=" N ILE A 350 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR A 317 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 352 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN A 385 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS A 355 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 387 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 641 through 644 Processing sheet with id= E, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.406A pdb=" N THR B 521 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE B 438 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY B 523 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR B 440 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLY B 525 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 526 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 184 through 186 Processing sheet with id= G, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.630A pdb=" N ILE B 350 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N TYR B 317 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 352 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN B 385 " --> pdb=" O TRP B 353 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS B 355 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU B 387 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 641 through 644 Processing sheet with id= I, first strand: chain 'B' and resid 677 through 680 378 hydrogen bonds defined for protein. 1116 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: 2.85 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3230 1.34 - 1.46: 2040 1.46 - 1.58: 4522 1.58 - 1.69: 15 1.69 - 1.81: 98 Bond restraints: 9905 Sorted by residual: bond pdb=" CA ILE B 453 " pdb=" CB ILE B 453 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 7.51e-01 bond pdb=" CA GLY B 538 " pdb=" C GLY B 538 " ideal model delta sigma weight residual 1.514 1.526 -0.012 1.41e-02 5.03e+03 6.85e-01 bond pdb=" N GLY A 523 " pdb=" CA GLY A 523 " ideal model delta sigma weight residual 1.452 1.442 0.010 1.40e-02 5.10e+03 5.17e-01 bond pdb=" C VAL B 516 " pdb=" O VAL B 516 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.19e-02 7.06e+03 5.02e-01 bond pdb=" CG1 ILE A 197 " pdb=" CD1 ILE A 197 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.88e-01 ... (remaining 9900 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.63: 275 106.63 - 113.47: 5311 113.47 - 120.31: 3641 120.31 - 127.15: 4067 127.15 - 133.99: 111 Bond angle restraints: 13405 Sorted by residual: angle pdb=" C ASN A 308 " pdb=" N GLN A 309 " pdb=" CA GLN A 309 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" CA LEU B 536 " pdb=" CB LEU B 536 " pdb=" CG LEU B 536 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.17e+00 angle pdb=" CA VAL B 516 " pdb=" C VAL B 516 " pdb=" N ILE B 517 " ideal model delta sigma weight residual 116.60 120.23 -3.63 1.45e+00 4.76e-01 6.28e+00 angle pdb=" N TYR A 407 " pdb=" CA TYR A 407 " pdb=" C TYR A 407 " ideal model delta sigma weight residual 110.19 107.15 3.04 1.24e+00 6.50e-01 6.00e+00 angle pdb=" CA VAL A 516 " pdb=" C VAL A 516 " pdb=" N ILE A 517 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.33e+00 ... (remaining 13400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 5845 35.43 - 70.86: 71 70.86 - 106.29: 8 106.29 - 141.71: 2 141.71 - 177.14: 2 Dihedral angle restraints: 5928 sinusoidal: 2432 harmonic: 3496 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 124.54 177.14 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 802 " pdb=" C1' TTP B 802 " pdb=" N1 TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sinusoidal sigma weight residual 301.68 125.82 175.87 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' TTP A 801 " pdb=" O5' TTP A 801 " pdb=" PA TTP A 801 " pdb=" O3A TTP A 801 " ideal model delta sinusoidal sigma weight residual 179.97 42.01 137.96 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 5925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 835 0.030 - 0.059: 381 0.059 - 0.089: 141 0.089 - 0.119: 66 0.119 - 0.148: 11 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CG LEU B 536 " pdb=" CB LEU B 536 " pdb=" CD1 LEU B 536 " pdb=" CD2 LEU B 536 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA VAL A 613 " pdb=" N VAL A 613 " pdb=" C VAL A 613 " pdb=" CB VAL A 613 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE B 703 " pdb=" N ILE B 703 " pdb=" C ILE B 703 " pdb=" CB ILE B 703 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1431 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 295 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C PHE B 295 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE B 295 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 296 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 277 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C GLU B 277 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU B 277 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN B 278 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 231 " 0.014 2.00e-02 2.50e+03 8.84e-03 1.56e+00 pdb=" CG TYR B 231 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 231 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 231 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 231 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 231 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 231 " 0.003 2.00e-02 2.50e+03 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 174 2.68 - 3.23: 9745 3.23 - 3.79: 16371 3.79 - 4.34: 23118 4.34 - 4.90: 37009 Nonbonded interactions: 86417 Sorted by model distance: nonbonded pdb=" O3G TTP A 801 " pdb="MG MG B 801 " model vdw 2.120 2.170 nonbonded pdb=" OE1 GLN A 290 " pdb="MG MG A 802 " model vdw 2.172 2.170 nonbonded pdb=" OD1 ASN B 674 " pdb=" NH1 ARG B 708 " model vdw 2.232 2.520 nonbonded pdb=" OD1 ASN B 652 " pdb=" OG SER B 654 " model vdw 2.235 2.440 nonbonded pdb=" OD1 ASP A 468 " pdb=" NH1 ARG A 561 " model vdw 2.236 2.520 ... (remaining 86412 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: 3.540 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: 12.950 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.470 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 : 0.003 0.027 9905 Z= 0.167 Angle : 0.541 10.597 13405 Z= 0.293 Chirality : 0.041 0.148 1434 Planarity : 0.003 0.030 1737 Dihedral : 12.819 177.141 3686 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 3.01 % Allowed : 5.83 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1195 helix: 1.41 (0.22), residues: 563 sheet: 0.24 (0.51), residues: 109 loop : -1.20 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 720 HIS 0.004 0.001 HIS A 540 PHE 0.010 0.001 PHE B 224 TYR 0.020 0.001 TYR B 231 ARG 0.003 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 278 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 292 MET cc_start: 0.8366 (mmp) cc_final: 0.7631 (mmp) REVERT: B 546 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5868 (pptt) outliers start: 31 outliers final: 4 residues processed: 295 average time/residue: 1.1543 time to fit residues: 365.5721 Evaluate side-chains 231 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 48 optimal weight: 0.0000 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 0.0970 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 455 ASN A 483 GLN A 492 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 290 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 388 ASN B 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9905 Z= 0.208 Angle : 0.543 6.803 13405 Z= 0.277 Chirality : 0.043 0.190 1434 Planarity : 0.004 0.036 1737 Dihedral : 11.641 176.236 1365 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.10 % Favored : 94.73 % Rotamer: Outliers : 3.01 % Allowed : 14.38 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1195 helix: 1.72 (0.22), residues: 562 sheet: -0.09 (0.49), residues: 108 loop : -1.14 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.006 0.001 HIS A 540 PHE 0.012 0.002 PHE A 482 TYR 0.020 0.001 TYR B 231 ARG 0.008 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7261 (ttpt) REVERT: B 351 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: B 537 ILE cc_start: 0.5041 (OUTLIER) cc_final: 0.4801 (mt) outliers start: 31 outliers final: 9 residues processed: 238 average time/residue: 1.1919 time to fit residues: 304.8645 Evaluate side-chains 225 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 605 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 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 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9905 Z= 0.320 Angle : 0.595 7.018 13405 Z= 0.305 Chirality : 0.045 0.153 1434 Planarity : 0.004 0.042 1737 Dihedral : 11.871 177.271 1363 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 3.60 % Allowed : 15.26 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1195 helix: 1.48 (0.22), residues: 557 sheet: -0.02 (0.49), residues: 108 loop : -1.14 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 PHE 0.018 0.002 PHE B 129 TYR 0.025 0.002 TYR B 231 ARG 0.008 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6898 (tm130) REVERT: B 161 LYS cc_start: 0.7527 (mtmt) cc_final: 0.7307 (ttpt) REVERT: B 351 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: B 537 ILE cc_start: 0.5099 (OUTLIER) cc_final: 0.4766 (mt) outliers start: 37 outliers final: 12 residues processed: 254 average time/residue: 1.1426 time to fit residues: 312.2327 Evaluate side-chains 233 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 218 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 605 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 548 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9905 Z= 0.183 Angle : 0.529 6.260 13405 Z= 0.270 Chirality : 0.042 0.139 1434 Planarity : 0.003 0.035 1737 Dihedral : 11.627 177.637 1363 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 3.40 % Allowed : 16.81 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1195 helix: 1.66 (0.22), residues: 562 sheet: 0.12 (0.49), residues: 108 loop : -1.11 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 PHE 0.013 0.001 PHE B 129 TYR 0.020 0.001 TYR B 231 ARG 0.006 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 218 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7322 (tttp) REVERT: A 590 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7156 (mtmm) REVERT: B 351 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7437 (mt0) REVERT: B 537 ILE cc_start: 0.4937 (OUTLIER) cc_final: 0.4621 (mt) outliers start: 35 outliers final: 14 residues processed: 233 average time/residue: 1.2324 time to fit residues: 307.1069 Evaluate side-chains 229 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 719 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 1 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9905 Z= 0.266 Angle : 0.571 6.693 13405 Z= 0.291 Chirality : 0.044 0.160 1434 Planarity : 0.004 0.037 1737 Dihedral : 11.760 178.099 1362 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 3.60 % Allowed : 16.81 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1195 helix: 1.57 (0.22), residues: 557 sheet: 0.13 (0.49), residues: 108 loop : -1.13 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.006 0.001 HIS A 540 PHE 0.016 0.002 PHE B 129 TYR 0.024 0.002 TYR B 231 ARG 0.005 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.6840 (tm130) REVERT: B 351 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: B 537 ILE cc_start: 0.5074 (OUTLIER) cc_final: 0.4722 (mt) outliers start: 37 outliers final: 14 residues processed: 239 average time/residue: 1.1771 time to fit residues: 302.3093 Evaluate side-chains 233 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 216 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 719 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.0010 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 548 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9905 Z= 0.233 Angle : 0.559 6.714 13405 Z= 0.285 Chirality : 0.043 0.210 1434 Planarity : 0.004 0.037 1737 Dihedral : 11.684 177.458 1362 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 3.01 % Allowed : 17.59 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1195 helix: 1.62 (0.22), residues: 556 sheet: 0.19 (0.49), residues: 108 loop : -1.13 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 PHE 0.014 0.002 PHE A 482 TYR 0.022 0.001 TYR B 231 ARG 0.004 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7305 (mt) cc_final: 0.7084 (mt) REVERT: A 431 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 644 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 351 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: B 537 ILE cc_start: 0.5065 (OUTLIER) cc_final: 0.4742 (mt) outliers start: 31 outliers final: 16 residues processed: 235 average time/residue: 1.2472 time to fit residues: 314.8591 Evaluate side-chains 228 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 719 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.0010 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 594 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9905 Z= 0.211 Angle : 0.555 6.940 13405 Z= 0.283 Chirality : 0.043 0.163 1434 Planarity : 0.004 0.036 1737 Dihedral : 11.609 177.593 1362 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 2.72 % Allowed : 18.37 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1195 helix: 1.66 (0.22), residues: 556 sheet: 0.31 (0.50), residues: 108 loop : -1.11 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 PHE 0.013 0.001 PHE B 129 TYR 0.022 0.001 TYR B 231 ARG 0.004 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7300 (mt) cc_final: 0.7037 (mt) REVERT: A 431 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8230 (mm) REVERT: A 548 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.6811 (tm130) REVERT: B 351 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: B 537 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.4693 (mt) outliers start: 28 outliers final: 14 residues processed: 230 average time/residue: 1.2018 time to fit residues: 296.7331 Evaluate side-chains 228 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 719 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 57 optimal weight: 0.0010 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 105 optimal weight: 0.0370 overall best weight: 0.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 594 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9905 Z= 0.156 Angle : 0.529 6.854 13405 Z= 0.269 Chirality : 0.042 0.192 1434 Planarity : 0.003 0.034 1737 Dihedral : 11.413 179.548 1362 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 2.24 % Allowed : 19.24 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1195 helix: 1.81 (0.22), residues: 555 sheet: 0.42 (0.51), residues: 107 loop : -1.05 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 720 HIS 0.004 0.001 HIS B 675 PHE 0.009 0.001 PHE A 526 TYR 0.018 0.001 TYR B 231 ARG 0.004 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8188 (mm) REVERT: B 351 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: B 537 ILE cc_start: 0.4940 (OUTLIER) cc_final: 0.4603 (mt) outliers start: 23 outliers final: 15 residues processed: 228 average time/residue: 1.1460 time to fit residues: 280.7067 Evaluate side-chains 231 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 719 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 71.163 > 50: distance: 47 - 51: 34.714 distance: 52 - 53: 39.193 distance: 53 - 54: 39.217 distance: 53 - 57: 41.236 distance: 57 - 58: 39.772 distance: 58 - 61: 40.222 distance: 59 - 60: 39.033 distance: 59 - 66: 49.937 distance: 60 - 89: 55.779 distance: 63 - 65: 40.324 distance: 66 - 67: 29.192 distance: 67 - 68: 39.676 distance: 69 - 98: 3.112 distance: 71 - 72: 39.818 distance: 72 - 73: 56.336 distance: 73 - 74: 68.837 distance: 75 - 76: 20.448 distance: 76 - 77: 19.922 distance: 76 - 79: 44.329 distance: 78 - 106: 42.798 distance: 81 - 82: 40.180 distance: 81 - 84: 39.486 distance: 83 - 110: 57.700 distance: 89 - 90: 29.192 distance: 90 - 91: 9.478 distance: 90 - 93: 10.801 distance: 92 - 118: 3.191 distance: 95 - 97: 39.062 distance: 99 - 100: 40.123 distance: 99 - 102: 39.171 distance: 100 - 101: 39.115 distance: 101 - 127: 35.860 distance: 103 - 104: 40.424 distance: 103 - 105: 56.431 distance: 107 - 108: 38.737 distance: 108 - 109: 40.826 distance: 108 - 110: 40.151 distance: 109 - 135: 32.700 distance: 110 - 111: 38.995 distance: 111 - 112: 39.693 distance: 111 - 114: 13.439 distance: 112 - 113: 37.803 distance: 112 - 118: 38.044 distance: 113 - 142: 35.735 distance: 114 - 115: 42.606 distance: 115 - 116: 39.313 distance: 115 - 117: 39.426 distance: 118 - 119: 23.428 distance: 119 - 120: 40.871 distance: 119 - 122: 18.349 distance: 120 - 121: 23.641 distance: 120 - 127: 16.047 distance: 121 - 149: 34.224