Starting phenix.real_space_refine (version: dev) on Sun Feb 19 00:09:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/02_2023/6pcv_20308.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/02_2023/6pcv_20308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/02_2023/6pcv_20308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/02_2023/6pcv_20308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/02_2023/6pcv_20308.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/02_2023/6pcv_20308.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 Process input model Symmetric amino acids flipped Residue "A ARG 516": "NH1" <-> "NH2" Residue "A TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ASP 847": "OD1" <-> "OD2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 1355": "OE1" <-> "OE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A ASP 1362": "OD1" <-> "OD2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A GLU 1391": "OE1" <-> "OE2" Residue "A ASP 1407": "OD1" <-> "OD2" Residue "A ASP 1417": "OD1" <-> "OD2" Residue "A PHE 1468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A ASP 1488": "OD1" <-> "OD2" Residue "A ASP 1492": "OD1" <-> "OD2" Residue "A TYR 1504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1540": "OD1" <-> "OD2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9035 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5946 Classifications: {'peptide': 754} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 718} Chain breaks: 6 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Time building chain proxies: 5.55, per 1000 atoms: 0.61 Number of scatterers: 9035 At special positions: 0 Unit cell: (81, 105, 108, 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 65 16.00 O 1708 8.00 N 1596 7.00 C 5666 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: 3.45 Conformation dependent library (CDL) restraints added in 1.5 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 33.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 545 through 556 Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 680 through 694 Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 791 through 803 Processing helix chain 'A' and resid 879 through 895 Processing helix chain 'A' and resid 933 through 947 removed outlier: 4.166A pdb=" N ARG A 947 " --> pdb=" O GLN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 removed outlier: 3.622A pdb=" N PHE A 967 " --> pdb=" O GLY A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1347 removed outlier: 3.985A pdb=" N ALA A1333 " --> pdb=" O GLN A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1375 Processing helix chain 'A' and resid 1389 through 1407 Processing helix chain 'A' and resid 1444 through 1450 Processing helix chain 'A' and resid 1454 through 1458 removed outlier: 3.598A pdb=" N GLY A1457 " --> pdb=" O ARG A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1518 removed outlier: 4.311A pdb=" N ALA A1486 " --> pdb=" O GLY A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1551 removed outlier: 5.080A pdb=" N ARG A1534 " --> pdb=" O ASP A1530 " (cutoff:3.500A) Proline residue: A1535 - end of helix removed outlier: 3.934A pdb=" N ALA A1538 " --> pdb=" O ARG A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1575 removed outlier: 3.627A pdb=" N ILE A1567 " --> pdb=" O GLY A1563 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A1569 " --> pdb=" O ILE A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1605 Processing helix chain 'A' and resid 1612 through 1623 removed outlier: 3.913A pdb=" N ARG A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1634 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 25 Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA3, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.446A pdb=" N LEU A 701 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 671 " --> pdb=" O ARG A 699 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG A 699 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 702 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 617 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU A 858 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 866 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 981 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 16.226A pdb=" N ALA A1577 " --> pdb=" O TYR A1017 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N GLN A1019 " --> pdb=" O ALA A1577 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N GLN A1579 " --> pdb=" O GLN A1019 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS A1021 " --> pdb=" O GLN A1579 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL A1581 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A1023 " --> pdb=" O VAL A1581 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N CYS A1583 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET A1025 " --> pdb=" O CYS A1583 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A1377 " --> pdb=" O CYS A1578 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET A1580 " --> pdb=" O LEU A1377 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS A1379 " --> pdb=" O MET A1580 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET A1582 " --> pdb=" O HIS A1379 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN A1381 " --> pdb=" O MET A1582 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL A1409 " --> pdb=" O LEU A1463 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR A1410 " --> pdb=" O VAL A1439 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE A1441 " --> pdb=" O THR A1410 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER A1412 " --> pdb=" O PHE A1441 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU A1443 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS A1414 " --> pdb=" O LEU A1443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 640 removed outlier: 6.731A pdb=" N ASP A 638 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 707 through 713 removed outlier: 7.325A pdb=" N THR A 843 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL A 754 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A 845 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 721 through 725 removed outlier: 6.377A pdb=" N GLN A 722 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.751A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.675A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.246A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.251A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.659A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.607A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.141A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 3.75 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: 3005 1.34 - 1.46: 1648 1.46 - 1.58: 4458 1.58 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 9202 Sorted by residual: bond pdb=" CB VAL A 856 " pdb=" CG2 VAL A 856 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" C SER A 949 " pdb=" N PRO A 950 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.94e+00 bond pdb=" CG LEU A1383 " pdb=" CD1 LEU A1383 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" C PRO A 950 " pdb=" N PRO A 951 " ideal model delta sigma weight residual 1.338 1.365 -0.027 1.90e-02 2.77e+03 2.05e+00 bond pdb=" C ALA A 764 " pdb=" N PRO A 765 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.23e-02 6.61e+03 1.96e+00 ... (remaining 9197 not shown) Histogram of bond angle deviations from ideal: 98.59 - 107.48: 363 107.48 - 116.36: 5821 116.36 - 125.24: 6105 125.24 - 134.13: 155 134.13 - 143.01: 1 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C PRO A 950 " pdb=" N PRO A 951 " pdb=" CA PRO A 951 " ideal model delta sigma weight residual 127.00 143.01 -16.01 2.40e+00 1.74e-01 4.45e+01 angle pdb=" C LEU A1564 " pdb=" N ILE A1565 " pdb=" CA ILE A1565 " ideal model delta sigma weight residual 120.24 124.20 -3.96 6.30e-01 2.52e+00 3.95e+01 angle pdb=" C PRO A 950 " pdb=" N PRO A 951 " pdb=" CD PRO A 951 " ideal model delta sigma weight residual 120.60 107.89 12.71 2.20e+00 2.07e-01 3.34e+01 angle pdb=" N PRO A 950 " pdb=" CA PRO A 950 " pdb=" C PRO A 950 " ideal model delta sigma weight residual 110.70 115.12 -4.42 1.22e+00 6.72e-01 1.31e+01 angle pdb=" N SER A 949 " pdb=" CA SER A 949 " pdb=" C SER A 949 " ideal model delta sigma weight residual 109.81 117.53 -7.72 2.21e+00 2.05e-01 1.22e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5045 17.84 - 35.69: 438 35.69 - 53.53: 78 53.53 - 71.38: 17 71.38 - 89.22: 8 Dihedral angle restraints: 5586 sinusoidal: 2233 harmonic: 3353 Sorted by residual: dihedral pdb=" CA TYR A1420 " pdb=" C TYR A1420 " pdb=" N VAL A1421 " pdb=" CA VAL A1421 " ideal model delta harmonic sigma weight residual 180.00 156.79 23.21 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA VAL A1421 " pdb=" C VAL A1421 " pdb=" N ALA A1422 " pdb=" CA ALA A1422 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ARG A1626 " pdb=" C ARG A1626 " pdb=" N VAL A1627 " pdb=" CA VAL A1627 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 918 0.050 - 0.100: 345 0.100 - 0.150: 99 0.150 - 0.200: 24 0.200 - 0.250: 6 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CB ILE A 529 " pdb=" CA ILE A 529 " pdb=" CG1 ILE A 529 " pdb=" CG2 ILE A 529 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 873 " pdb=" CA ILE A 873 " pdb=" CG1 ILE A 873 " pdb=" CG2 ILE A 873 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1389 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 712 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 713 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 713 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 713 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1480 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A1481 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A1481 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1481 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO B 236 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.035 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1680 2.77 - 3.30: 8280 3.30 - 3.83: 15757 3.83 - 4.37: 18379 4.37 - 4.90: 31956 Nonbonded interactions: 76052 Sorted by model distance: nonbonded pdb=" OG SER A1359 " pdb=" OD1 ASP A1362 " model vdw 2.235 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.289 2.440 nonbonded pdb=" O ASP A1398 " pdb=" OG1 THR A1402 " model vdw 2.289 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.302 2.440 ... (remaining 76047 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5666 2.51 5 N 1596 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.540 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: 6.240 Check model and map are aligned: 0.130 Process input model: 27.260 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.006 0.061 9202 Z= 0.386 Angle : 0.978 16.008 12445 Z= 0.530 Chirality : 0.059 0.250 1392 Planarity : 0.007 0.065 1621 Dihedral : 14.309 89.224 3416 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.20), residues: 1137 helix: -2.19 (0.19), residues: 383 sheet: -2.10 (0.28), residues: 249 loop : -2.20 (0.25), residues: 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 335 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 339 average time/residue: 0.3076 time to fit residues: 134.1241 Evaluate side-chains 274 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0883 time to fit residues: 2.0263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS A 573 ASN A 643 ASN A 749 GLN A 802 GLN A 975 ASN A1415 GLN A1490 GLN A1503 GLN A1588 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 35 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 9202 Z= 0.259 Angle : 0.673 8.895 12445 Z= 0.350 Chirality : 0.045 0.246 1392 Planarity : 0.005 0.058 1621 Dihedral : 5.164 27.083 1255 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.73 (0.24), residues: 1137 helix: 0.03 (0.25), residues: 384 sheet: -1.76 (0.29), residues: 260 loop : -1.65 (0.27), residues: 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 279 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 12 residues processed: 302 average time/residue: 0.2970 time to fit residues: 117.8099 Evaluate side-chains 274 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 262 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1000 time to fit residues: 3.6586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9202 Z= 0.270 Angle : 0.670 9.025 12445 Z= 0.345 Chirality : 0.045 0.196 1392 Planarity : 0.005 0.059 1621 Dihedral : 4.890 23.553 1255 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.06 (0.25), residues: 1137 helix: 0.87 (0.27), residues: 382 sheet: -1.66 (0.28), residues: 275 loop : -1.31 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 279 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 294 average time/residue: 0.2590 time to fit residues: 99.3696 Evaluate side-chains 277 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 262 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0908 time to fit residues: 3.9088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 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 749 GLN A 770 HIS ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1502 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 9202 Z= 0.247 Angle : 0.670 8.078 12445 Z= 0.341 Chirality : 0.045 0.168 1392 Planarity : 0.005 0.052 1621 Dihedral : 4.798 21.298 1255 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.78 (0.25), residues: 1137 helix: 1.09 (0.27), residues: 383 sheet: -1.50 (0.29), residues: 271 loop : -1.15 (0.29), residues: 483 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 276 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 288 average time/residue: 0.2621 time to fit residues: 99.4058 Evaluate side-chains 260 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 246 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0974 time to fit residues: 3.9190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 749 GLN ** A1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN ** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 9202 Z= 0.283 Angle : 0.694 10.001 12445 Z= 0.351 Chirality : 0.046 0.196 1392 Planarity : 0.005 0.048 1621 Dihedral : 4.758 21.429 1255 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.69 (0.25), residues: 1137 helix: 1.13 (0.27), residues: 389 sheet: -1.46 (0.29), residues: 271 loop : -1.10 (0.29), residues: 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 262 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 270 average time/residue: 0.2618 time to fit residues: 93.3379 Evaluate side-chains 260 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0941 time to fit residues: 2.8939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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: 68.1473 > 50: distance: 35 - 40: 10.732 distance: 40 - 41: 7.008 distance: 41 - 42: 10.573 distance: 41 - 44: 6.611 distance: 42 - 43: 9.539 distance: 42 - 46: 7.373 distance: 44 - 45: 7.035 distance: 46 - 47: 38.753 distance: 46 - 52: 12.453 distance: 47 - 48: 58.342 distance: 47 - 50: 49.580 distance: 48 - 49: 40.022 distance: 48 - 53: 46.664 distance: 50 - 51: 29.450 distance: 51 - 52: 16.818 distance: 53 - 54: 12.119 distance: 53 - 59: 45.741 distance: 54 - 55: 33.190 distance: 54 - 57: 31.362 distance: 55 - 56: 46.094 distance: 55 - 60: 49.639 distance: 57 - 58: 34.007 distance: 58 - 59: 33.721 distance: 60 - 61: 35.810 distance: 61 - 62: 33.586 distance: 61 - 64: 43.461 distance: 62 - 63: 39.750 distance: 62 - 71: 26.033 distance: 64 - 65: 36.177 distance: 65 - 66: 18.773 distance: 65 - 67: 23.755 distance: 66 - 68: 15.829 distance: 67 - 69: 26.406 distance: 68 - 70: 12.302 distance: 69 - 70: 17.648 distance: 71 - 72: 65.909 distance: 72 - 73: 43.247 distance: 72 - 75: 45.604 distance: 73 - 74: 57.441 distance: 73 - 80: 7.828 distance: 75 - 76: 53.383 distance: 76 - 77: 45.128 distance: 77 - 78: 15.334 distance: 78 - 79: 13.757 distance: 80 - 81: 39.499 distance: 81 - 82: 30.346 distance: 81 - 84: 41.244 distance: 82 - 83: 40.319 distance: 82 - 89: 58.460 distance: 84 - 85: 56.118 distance: 85 - 86: 47.206 distance: 86 - 87: 39.493 distance: 86 - 88: 50.199 distance: 89 - 90: 27.593 distance: 90 - 91: 37.055 distance: 90 - 93: 39.179 distance: 91 - 92: 50.527 distance: 91 - 94: 51.241 distance: 94 - 95: 29.742 distance: 94 - 100: 43.686 distance: 95 - 96: 43.913 distance: 95 - 98: 35.654 distance: 96 - 97: 49.144 distance: 96 - 101: 30.283 distance: 98 - 99: 23.178 distance: 99 - 100: 27.269 distance: 101 - 102: 32.838 distance: 102 - 103: 25.704 distance: 102 - 105: 35.644 distance: 103 - 104: 30.304 distance: 103 - 109: 58.019 distance: 105 - 106: 35.900 distance: 106 - 107: 23.768 distance: 106 - 108: 20.366 distance: 109 - 110: 51.672 distance: 110 - 111: 30.146 distance: 110 - 113: 49.036 distance: 111 - 112: 51.510 distance: 111 - 118: 33.341 distance: 113 - 114: 60.528 distance: 114 - 115: 24.854 distance: 115 - 116: 5.436 distance: 115 - 117: 20.388