Starting phenix.real_space_refine on Sun Aug 4 01:35:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/08_2024/6qvd_4649.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/08_2024/6qvd_4649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/08_2024/6qvd_4649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/08_2024/6qvd_4649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/08_2024/6qvd_4649.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvd_4649/08_2024/6qvd_4649.cif" } resolution = 4.34 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= 0.003 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6094 2.51 5 N 1472 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 199": "NH1" <-> "NH2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 858": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9212 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4606 Classifications: {'peptide': 596} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 567} Chain breaks: 2 Chain: "A" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4606 Classifications: {'peptide': 596} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 567} Chain breaks: 2 Time building chain proxies: 5.90, per 1000 atoms: 0.64 Number of scatterers: 9212 At special positions: 0 Unit cell: (101.65, 95.23, 108.07, 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 70 16.00 O 1576 8.00 N 1472 7.00 C 6094 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: 3.90 Conformation dependent library (CDL) restraints added in 1.7 seconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 66.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 115 through 154 removed outlier: 4.768A pdb=" N GLN B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.359A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.785A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.614A pdb=" N PHE B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.582A pdb=" N GLY B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 323 removed outlier: 4.103A pdb=" N ARG B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 377 removed outlier: 3.572A pdb=" N PHE B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 3.791A pdb=" N SER B 383 " --> pdb=" O HIS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 403 removed outlier: 4.557A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.571A pdb=" N ALA B 447 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 removed outlier: 3.503A pdb=" N ILE B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.572A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.948A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 585 Processing helix chain 'B' and resid 621 through 632 Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'A' and resid 116 through 154 removed outlier: 4.768A pdb=" N GLN A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.360A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.784A pdb=" N PHE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.613A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.581A pdb=" N GLY A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 323 removed outlier: 4.102A pdb=" N ARG A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 377 removed outlier: 3.572A pdb=" N PHE A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.792A pdb=" N SER A 383 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.557A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.570A pdb=" N ALA A 447 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 450 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.504A pdb=" N ILE A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 4.572A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.949A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 871 Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640 removed outlier: 5.569A pdb=" N LEU B 637 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 651 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 639 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 651 " --> pdb=" O ASP B 822 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B 822 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.553A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640 removed outlier: 5.569A pdb=" N LEU A 637 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 651 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 639 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 651 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A 822 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 6.553A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1623 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: 2.87 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1631 1.32 - 1.45: 2434 1.45 - 1.57: 5257 1.57 - 1.69: 4 1.69 - 1.81: 116 Bond restraints: 9442 Sorted by residual: bond pdb=" CB LYS B 518 " pdb=" CG LYS B 518 " ideal model delta sigma weight residual 1.520 1.628 -0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CB LYS A 518 " pdb=" CG LYS A 518 " ideal model delta sigma weight residual 1.520 1.628 -0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CG1 ILE B 516 " pdb=" CD1 ILE B 516 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.12e+00 bond pdb=" CG1 ILE A 516 " pdb=" CD1 ILE A 516 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 7.00e+00 bond pdb=" CA TYR B 589 " pdb=" C TYR B 589 " ideal model delta sigma weight residual 1.523 1.556 -0.033 1.34e-02 5.57e+03 5.96e+00 ... (remaining 9437 not shown) Histogram of bond angle deviations from ideal: 94.02 - 103.24: 118 103.24 - 112.46: 4668 112.46 - 121.68: 6102 121.68 - 130.90: 1867 130.90 - 140.12: 75 Bond angle restraints: 12830 Sorted by residual: angle pdb=" C PRO B 588 " pdb=" N TYR B 589 " pdb=" CA TYR B 589 " ideal model delta sigma weight residual 121.54 140.12 -18.58 1.91e+00 2.74e-01 9.47e+01 angle pdb=" C PRO A 588 " pdb=" N TYR A 589 " pdb=" CA TYR A 589 " ideal model delta sigma weight residual 121.54 140.12 -18.58 1.91e+00 2.74e-01 9.46e+01 angle pdb=" N ILE B 510 " pdb=" CA ILE B 510 " pdb=" C ILE B 510 " ideal model delta sigma weight residual 108.82 120.55 -11.73 1.22e+00 6.72e-01 9.25e+01 angle pdb=" N ILE A 510 " pdb=" CA ILE A 510 " pdb=" C ILE A 510 " ideal model delta sigma weight residual 108.82 120.53 -11.71 1.22e+00 6.72e-01 9.21e+01 angle pdb=" N TYR B 589 " pdb=" CA TYR B 589 " pdb=" C TYR B 589 " ideal model delta sigma weight residual 110.80 125.10 -14.30 2.13e+00 2.20e-01 4.51e+01 ... (remaining 12825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 4976 15.62 - 31.24: 396 31.24 - 46.87: 110 46.87 - 62.49: 20 62.49 - 78.11: 6 Dihedral angle restraints: 5508 sinusoidal: 2086 harmonic: 3422 Sorted by residual: dihedral pdb=" CA GLY A 594 " pdb=" C GLY A 594 " pdb=" N TRP A 595 " pdb=" CA TRP A 595 " ideal model delta harmonic sigma weight residual 180.00 125.75 54.25 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA GLY B 594 " pdb=" C GLY B 594 " pdb=" N TRP B 595 " pdb=" CA TRP B 595 " ideal model delta harmonic sigma weight residual 180.00 125.77 54.23 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA LYS B 324 " pdb=" C LYS B 324 " pdb=" N ASP B 325 " pdb=" CA ASP B 325 " ideal model delta harmonic sigma weight residual -180.00 -140.86 -39.14 0 5.00e+00 4.00e-02 6.13e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1194 0.104 - 0.208: 256 0.208 - 0.312: 54 0.312 - 0.416: 10 0.416 - 0.520: 4 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CG LEU B 427 " pdb=" CB LEU B 427 " pdb=" CD1 LEU B 427 " pdb=" CD2 LEU B 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CG LEU A 427 " pdb=" CB LEU A 427 " pdb=" CD1 LEU A 427 " pdb=" CD2 LEU A 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CB ILE B 329 " pdb=" CA ILE B 329 " pdb=" CG1 ILE B 329 " pdb=" CG2 ILE B 329 " both_signs ideal model delta sigma weight residual False 2.64 3.07 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 1515 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 508 " 0.047 2.00e-02 2.50e+03 9.25e-02 8.56e+01 pdb=" C ASP A 508 " -0.160 2.00e-02 2.50e+03 pdb=" O ASP A 508 " 0.059 2.00e-02 2.50e+03 pdb=" N GLY A 509 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 508 " -0.047 2.00e-02 2.50e+03 9.20e-02 8.47e+01 pdb=" C ASP B 508 " 0.159 2.00e-02 2.50e+03 pdb=" O ASP B 508 " -0.058 2.00e-02 2.50e+03 pdb=" N GLY B 509 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 588 " 0.028 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C PRO B 588 " -0.101 2.00e-02 2.50e+03 pdb=" O PRO B 588 " 0.038 2.00e-02 2.50e+03 pdb=" N TYR B 589 " 0.035 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 895 2.73 - 3.28: 9696 3.28 - 3.82: 16348 3.82 - 4.36: 17975 4.36 - 4.90: 28730 Nonbonded interactions: 73644 Sorted by model distance: nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.193 3.040 nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.194 3.040 nonbonded pdb=" O CYS A 179 " pdb=" OG SER A 183 " model vdw 2.219 3.040 nonbonded pdb=" O CYS B 179 " pdb=" OG SER B 183 " model vdw 2.220 3.040 nonbonded pdb=" O SER B 289 " pdb=" OG1 THR B 293 " model vdw 2.235 3.040 ... (remaining 73639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.140 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.010 0.108 9442 Z= 0.615 Angle : 1.807 19.518 12830 Z= 0.948 Chirality : 0.096 0.520 1518 Planarity : 0.012 0.093 1568 Dihedral : 12.959 78.110 3308 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.58 % Favored : 90.08 % Rotamer: Outliers : 3.61 % Allowed : 10.62 % Favored : 85.77 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 3.85 % Twisted General : 0.88 % 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: -4.01 (0.20), residues: 1180 helix: -2.27 (0.15), residues: 764 sheet: -0.92 (0.99), residues: 20 loop : -3.28 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.007 TRP A 469 HIS 0.008 0.003 HIS A 389 PHE 0.070 0.007 PHE B 464 TYR 0.046 0.005 TYR B 146 ARG 0.008 0.002 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.9271 (ptp) cc_final: 0.8957 (ptt) REVERT: B 307 PHE cc_start: 0.9356 (t80) cc_final: 0.8903 (t80) REVERT: B 315 VAL cc_start: 0.9594 (t) cc_final: 0.9358 (m) REVERT: B 339 MET cc_start: 0.8880 (ptp) cc_final: 0.8608 (pmm) REVERT: B 341 PHE cc_start: 0.8529 (t80) cc_final: 0.7624 (t80) REVERT: B 404 PHE cc_start: 0.9225 (m-10) cc_final: 0.8834 (m-80) REVERT: B 464 PHE cc_start: 0.8934 (p90) cc_final: 0.8558 (p90) REVERT: B 468 PHE cc_start: 0.9021 (m-10) cc_final: 0.8714 (m-10) REVERT: B 470 MET cc_start: 0.9282 (ttm) cc_final: 0.8977 (ttm) REVERT: B 494 PHE cc_start: 0.9483 (t80) cc_final: 0.9240 (t80) REVERT: B 559 MET cc_start: 0.9772 (ppp) cc_final: 0.9202 (ppp) REVERT: B 643 LYS cc_start: 0.9606 (pttp) cc_final: 0.9013 (mmmt) REVERT: A 135 MET cc_start: 0.9200 (ptp) cc_final: 0.8909 (ptt) REVERT: A 307 PHE cc_start: 0.9322 (t80) cc_final: 0.8773 (t80) REVERT: A 315 VAL cc_start: 0.9607 (t) cc_final: 0.9378 (m) REVERT: A 339 MET cc_start: 0.9040 (ptp) cc_final: 0.8418 (pmm) REVERT: A 341 PHE cc_start: 0.8824 (t80) cc_final: 0.8351 (t80) REVERT: A 404 PHE cc_start: 0.9420 (m-10) cc_final: 0.9077 (m-80) REVERT: A 427 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (tp) REVERT: A 435 LYS cc_start: 0.9716 (mmtt) cc_final: 0.9429 (tptp) REVERT: A 464 PHE cc_start: 0.8895 (p90) cc_final: 0.8557 (p90) REVERT: A 468 PHE cc_start: 0.8983 (m-10) cc_final: 0.8774 (m-80) REVERT: A 470 MET cc_start: 0.9224 (ttm) cc_final: 0.8800 (ttm) REVERT: A 494 PHE cc_start: 0.9325 (t80) cc_final: 0.8951 (t80) REVERT: A 557 LEU cc_start: 0.9664 (mm) cc_final: 0.9399 (tt) REVERT: A 559 MET cc_start: 0.9823 (ppp) cc_final: 0.9371 (ppp) outliers start: 36 outliers final: 10 residues processed: 233 average time/residue: 0.2070 time to fit residues: 67.0475 Evaluate side-chains 155 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9442 Z= 0.295 Angle : 0.944 11.820 12830 Z= 0.493 Chirality : 0.051 0.256 1518 Planarity : 0.006 0.065 1568 Dihedral : 7.312 34.344 1256 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1180 helix: -0.76 (0.17), residues: 766 sheet: -0.07 (0.86), residues: 20 loop : -2.76 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 469 HIS 0.005 0.001 HIS A 835 PHE 0.038 0.003 PHE A 464 TYR 0.018 0.002 TYR A 578 ARG 0.008 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.9145 (ptp) cc_final: 0.8742 (ptt) REVERT: B 341 PHE cc_start: 0.8280 (t80) cc_final: 0.7732 (t80) REVERT: B 404 PHE cc_start: 0.9257 (m-10) cc_final: 0.8897 (m-80) REVERT: B 410 MET cc_start: 0.9013 (tpt) cc_final: 0.8406 (tpt) REVERT: B 464 PHE cc_start: 0.8973 (p90) cc_final: 0.8211 (p90) REVERT: B 468 PHE cc_start: 0.8955 (m-10) cc_final: 0.8555 (m-80) REVERT: B 470 MET cc_start: 0.9284 (ttm) cc_final: 0.8743 (mtt) REVERT: B 494 PHE cc_start: 0.9465 (t80) cc_final: 0.9179 (t80) REVERT: B 568 MET cc_start: 0.9473 (ppp) cc_final: 0.9253 (ppp) REVERT: B 643 LYS cc_start: 0.9575 (pttp) cc_final: 0.8992 (mmmt) REVERT: A 122 VAL cc_start: 0.9267 (m) cc_final: 0.9027 (m) REVERT: A 135 MET cc_start: 0.9128 (ptp) cc_final: 0.8739 (ptt) REVERT: A 307 PHE cc_start: 0.9291 (t80) cc_final: 0.8994 (t80) REVERT: A 341 PHE cc_start: 0.8743 (t80) cc_final: 0.8274 (t80) REVERT: A 410 MET cc_start: 0.9042 (tpt) cc_final: 0.8692 (tpp) REVERT: A 436 HIS cc_start: 0.9165 (m-70) cc_final: 0.8876 (m-70) REVERT: A 470 MET cc_start: 0.9273 (ttm) cc_final: 0.8832 (tmm) REVERT: A 494 PHE cc_start: 0.9324 (t80) cc_final: 0.8878 (t80) REVERT: A 559 MET cc_start: 0.9798 (ppp) cc_final: 0.9515 (ppp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1952 time to fit residues: 49.7068 Evaluate side-chains 140 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS A 436 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9442 Z= 0.219 Angle : 0.830 10.072 12830 Z= 0.428 Chirality : 0.049 0.240 1518 Planarity : 0.006 0.052 1568 Dihedral : 6.570 32.302 1256 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.10 % Allowed : 7.01 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1180 helix: -0.08 (0.18), residues: 770 sheet: 0.24 (0.96), residues: 20 loop : -2.61 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 595 HIS 0.007 0.001 HIS A 835 PHE 0.030 0.003 PHE B 365 TYR 0.015 0.001 TYR A 137 ARG 0.003 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 VAL cc_start: 0.9084 (m) cc_final: 0.8841 (m) REVERT: B 303 TRP cc_start: 0.8763 (t60) cc_final: 0.8538 (t60) REVERT: B 307 PHE cc_start: 0.9256 (t80) cc_final: 0.9037 (t80) REVERT: B 339 MET cc_start: 0.9010 (ptp) cc_final: 0.8570 (ptp) REVERT: B 341 PHE cc_start: 0.8170 (t80) cc_final: 0.7656 (t80) REVERT: B 404 PHE cc_start: 0.9216 (m-10) cc_final: 0.8798 (m-80) REVERT: B 410 MET cc_start: 0.8923 (tpt) cc_final: 0.8291 (tpt) REVERT: B 464 PHE cc_start: 0.8989 (p90) cc_final: 0.8005 (p90) REVERT: B 468 PHE cc_start: 0.8859 (m-10) cc_final: 0.8505 (m-10) REVERT: B 477 MET cc_start: 0.8705 (ppp) cc_final: 0.8278 (ppp) REVERT: B 494 PHE cc_start: 0.9457 (t80) cc_final: 0.9137 (t80) REVERT: B 568 MET cc_start: 0.9474 (ppp) cc_final: 0.9252 (ppp) REVERT: B 643 LYS cc_start: 0.9532 (pttp) cc_final: 0.8962 (mmmt) REVERT: A 122 VAL cc_start: 0.9168 (m) cc_final: 0.8938 (m) REVERT: A 341 PHE cc_start: 0.8549 (t80) cc_final: 0.7969 (t80) REVERT: A 379 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7747 (t-90) REVERT: A 410 MET cc_start: 0.8994 (tpt) cc_final: 0.8647 (tpp) REVERT: A 494 PHE cc_start: 0.9268 (t80) cc_final: 0.8844 (t80) REVERT: A 559 MET cc_start: 0.9704 (ppp) cc_final: 0.9349 (ppp) REVERT: A 836 LYS cc_start: 0.9501 (mttt) cc_final: 0.9197 (tppt) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1934 time to fit residues: 50.9712 Evaluate side-chains 148 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.7085 > 50: distance: 31 - 36: 16.270 distance: 36 - 37: 22.046 distance: 37 - 38: 25.918 distance: 37 - 40: 20.223 distance: 38 - 39: 13.899 distance: 38 - 45: 36.724 distance: 40 - 41: 17.156 distance: 41 - 42: 19.883 distance: 42 - 43: 8.710 distance: 43 - 44: 13.739 distance: 45 - 46: 29.035 distance: 46 - 47: 10.393 distance: 47 - 48: 56.073 distance: 47 - 52: 17.450 distance: 49 - 51: 41.847 distance: 52 - 53: 15.567 distance: 53 - 54: 22.291 distance: 53 - 56: 37.089 distance: 54 - 55: 10.010 distance: 54 - 60: 17.958 distance: 56 - 57: 26.239 distance: 57 - 58: 5.789 distance: 60 - 61: 28.343 distance: 60 - 66: 39.774 distance: 61 - 62: 40.676 distance: 61 - 64: 9.485 distance: 62 - 63: 32.750 distance: 62 - 67: 20.218 distance: 64 - 65: 35.188 distance: 65 - 66: 39.986 distance: 67 - 68: 22.160 distance: 68 - 69: 5.831 distance: 68 - 71: 5.552 distance: 69 - 70: 10.704 distance: 69 - 75: 9.358 distance: 70 - 138: 29.259 distance: 71 - 72: 22.722 distance: 72 - 73: 8.768 distance: 72 - 74: 26.579 distance: 75 - 76: 4.246 distance: 76 - 77: 5.845 distance: 76 - 79: 26.747 distance: 77 - 78: 4.980 distance: 77 - 82: 8.556 distance: 79 - 80: 8.436 distance: 79 - 81: 40.399 distance: 82 - 83: 15.140 distance: 83 - 84: 26.667 distance: 83 - 86: 29.457 distance: 84 - 85: 10.018 distance: 84 - 90: 41.997 distance: 86 - 87: 5.702 distance: 87 - 88: 10.695 distance: 87 - 89: 33.028 distance: 90 - 91: 21.288 distance: 91 - 92: 4.550 distance: 91 - 94: 6.087 distance: 92 - 93: 16.688 distance: 92 - 96: 33.519 distance: 94 - 95: 22.372 distance: 96 - 97: 45.870 distance: 97 - 98: 11.776 distance: 97 - 100: 11.170 distance: 98 - 99: 19.276 distance: 98 - 105: 28.911 distance: 102 - 103: 34.414 distance: 103 - 104: 31.424 distance: 105 - 106: 24.555 distance: 106 - 107: 21.566 distance: 106 - 109: 40.314 distance: 107 - 108: 10.516 distance: 107 - 113: 29.516 distance: 109 - 110: 35.760 distance: 110 - 111: 45.165 distance: 110 - 112: 18.339