Starting phenix.real_space_refine on Thu Jun 12 03:32:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9c_39073/06_2025/8y9c_39073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9c_39073/06_2025/8y9c_39073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9c_39073/06_2025/8y9c_39073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9c_39073/06_2025/8y9c_39073.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9c_39073/06_2025/8y9c_39073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9c_39073/06_2025/8y9c_39073.cif" } resolution = 3.0 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= -0.001 sd= 0.117 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 31 5.16 5 C 8545 2.51 5 N 2126 2.21 5 O 2697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13400 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 12901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1609, 12901 Classifications: {'peptide': 1609} Link IDs: {'PTRANS': 36, 'TRANS': 1572} Chain breaks: 8 Chain: "A" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 498 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5665 SG CYS B 699 72.932 32.177 129.402 1.00 14.08 S Time building chain proxies: 8.21, per 1000 atoms: 0.61 Number of scatterers: 13400 At special positions: 0 Unit cell: (114.194, 107.73, 170.213, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 31 16.00 O 2697 8.00 N 2126 7.00 C 8545 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 - 3.00 Amino acid : True - 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: 3.56 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B 699 " pdb="ZN ZN B3001 " - pdb=" ND1 HIS B 654 " pdb="ZN ZN B3001 " - pdb=" NE2 HIS B 758 " 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 42.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 21 through 36 removed outlier: 3.682A pdb=" N VAL B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 63 Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.809A pdb=" N LYS B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 137 through 158 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 167 through 197 removed outlier: 3.537A pdb=" N PHE B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.501A pdb=" N SER B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 Processing helix chain 'B' and resid 243 through 248 removed outlier: 3.727A pdb=" N LYS B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 264 through 280 removed outlier: 3.597A pdb=" N VAL B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 325 Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.631A pdb=" N THR B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 Processing helix chain 'B' and resid 394 through 420 Proline residue: B 417 - end of helix Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.725A pdb=" N VAL B 457 " --> pdb=" O TYR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.949A pdb=" N THR B 468 " --> pdb=" O ASN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.743A pdb=" N TYR B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 524 through 540 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 588 through 602 removed outlier: 3.842A pdb=" N ASN B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 removed outlier: 3.606A pdb=" N SER B 642 " --> pdb=" O ASP B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 707 through 710 Processing helix chain 'B' and resid 711 through 728 removed outlier: 5.019A pdb=" N ASP B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS B 723 " --> pdb=" O ARG B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 734 No H-bonds generated for 'chain 'B' and resid 732 through 734' Processing helix chain 'B' and resid 765 through 776 Processing helix chain 'B' and resid 794 through 810 Processing helix chain 'B' and resid 815 through 839 Processing helix chain 'B' and resid 851 through 877 removed outlier: 3.581A pdb=" N ASN B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 935 removed outlier: 4.435A pdb=" N ASP B 935 " --> pdb=" O SER B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 971 Processing helix chain 'B' and resid 981 through 994 Processing helix chain 'B' and resid 1005 through 1018 Processing helix chain 'B' and resid 1055 through 1069 removed outlier: 3.515A pdb=" N GLU B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1077 removed outlier: 3.734A pdb=" N THR B1077 " --> pdb=" O THR B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1353 Processing helix chain 'B' and resid 1433 through 1440 Processing helix chain 'B' and resid 1440 through 1452 removed outlier: 4.064A pdb=" N GLY B1452 " --> pdb=" O ILE B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1559 through 1574 removed outlier: 3.548A pdb=" N GLY B1574 " --> pdb=" O MET B1570 " (cutoff:3.500A) Processing helix chain 'B' and resid 1580 through 1589 Processing helix chain 'B' and resid 1651 through 1653 No H-bonds generated for 'chain 'B' and resid 1651 through 1653' Processing helix chain 'B' and resid 1680 through 1683 Processing helix chain 'B' and resid 1685 through 1689 removed outlier: 3.535A pdb=" N VAL B1689 " --> pdb=" O ASP B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1737 through 1739 No H-bonds generated for 'chain 'B' and resid 1737 through 1739' Processing helix chain 'B' and resid 1777 through 1779 No H-bonds generated for 'chain 'B' and resid 1777 through 1779' Processing helix chain 'B' and resid 1793 through 1800 Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 39 through 57 removed outlier: 3.691A pdb=" N ARG A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 239 removed outlier: 6.179A pdb=" N LEU B 98 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE B 130 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 100 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE B 101 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN B 386 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N LYS B 375 " --> pdb=" O GLN B 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 290 through 291 Processing sheet with id=AA4, first strand: chain 'B' and resid 606 through 610 removed outlier: 6.216A pdb=" N VAL B 579 " --> pdb=" O LYS B 648 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 650 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR B 581 " --> pdb=" O THR B 650 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE B 652 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL B 583 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N HIS B 654 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS B 699 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 736 " --> pdb=" O PHE B 781 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE B 781 " --> pdb=" O ILE B 736 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 618 through 623 Processing sheet with id=AA6, first strand: chain 'B' and resid 745 through 747 Processing sheet with id=AA7, first strand: chain 'B' and resid 883 through 884 Processing sheet with id=AA8, first strand: chain 'B' and resid 883 through 884 Processing sheet with id=AA9, first strand: chain 'B' and resid 937 through 941 removed outlier: 6.683A pdb=" N VAL B 946 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 940 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1344 through 1346 Processing sheet with id=AB2, first strand: chain 'B' and resid 1460 through 1466 removed outlier: 3.778A pdb=" N TYR B1510 " --> pdb=" O ILE B1596 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1515 through 1521 removed outlier: 5.174A pdb=" N ASP B1516 " --> pdb=" O TYR B1531 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B1531 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B1526 " --> pdb=" O ILE B1545 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B1545 " --> pdb=" O ILE B1526 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LYS B1538 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B1558 " --> pdb=" O LYS B1538 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER B1540 " --> pdb=" O VAL B1556 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL B1556 " --> pdb=" O SER B1540 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B1542 " --> pdb=" O ASN B1554 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY B1555 " --> pdb=" O ASP B1608 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N ASN B1610 " --> pdb=" O GLY B1555 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N TYR B1557 " --> pdb=" O ASN B1610 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N ILE B1612 " --> pdb=" O TYR B1557 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE B1611 " --> pdb=" O CYS B1626 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS B1626 " --> pdb=" O PHE B1611 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN B1621 " --> pdb=" O ILE B1637 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B1637 " --> pdb=" O GLN B1621 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B1623 " --> pdb=" O TYR B1635 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1674 through 1678 removed outlier: 6.153A pdb=" N ILE B1675 " --> pdb=" O ASN B1704 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N THR B1706 " --> pdb=" O ILE B1675 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE B1677 " --> pdb=" O THR B1706 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE B1703 " --> pdb=" O ASN B1733 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B1730 " --> pdb=" O SER B1782 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN B1784 " --> pdb=" O ILE B1730 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE B1732 " --> pdb=" O ASN B1784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1815 through 1819 Processing sheet with id=AB6, first strand: chain 'B' and resid 1835 through 1839 Processing sheet with id=AB7, first strand: chain 'B' and resid 1856 through 1860 removed outlier: 3.948A pdb=" N ALA B1874 " --> pdb=" O ASN B1868 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1878 through 1882 Processing sheet with id=AB9, first strand: chain 'B' and resid 1898 through 1902 Processing sheet with id=AC1, first strand: chain 'B' and resid 1928 through 1932 Processing sheet with id=AC2, first strand: chain 'A' and resid 22 through 25 removed outlier: 6.340A pdb=" N PHE A 31 " --> pdb=" O ASP A 61 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1902 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: 6.40 Time building geometry restraints manager: 3.76 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: 4348 1.34 - 1.46: 2188 1.46 - 1.58: 7030 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 13621 Sorted by residual: bond pdb=" N ILE B 890 " pdb=" CA ILE B 890 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 8.97e+00 bond pdb=" N ILE B 885 " pdb=" CA ILE B 885 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" N GLY B1508 " pdb=" CA GLY B1508 " ideal model delta sigma weight residual 1.448 1.478 -0.030 1.12e-02 7.97e+03 7.29e+00 bond pdb=" N SER B1511 " pdb=" CA SER B1511 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.26e+00 bond pdb=" N PHE B1507 " pdb=" CA PHE B1507 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.85e+00 ... (remaining 13616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 18125 1.55 - 3.10: 245 3.10 - 4.65: 36 4.65 - 6.20: 11 6.20 - 7.75: 1 Bond angle restraints: 18418 Sorted by residual: angle pdb=" C PRO B1505 " pdb=" CA PRO B1505 " pdb=" CB PRO B1505 " ideal model delta sigma weight residual 110.92 106.23 4.69 1.22e+00 6.72e-01 1.48e+01 angle pdb=" N GLU B 888 " pdb=" CA GLU B 888 " pdb=" C GLU B 888 " ideal model delta sigma weight residual 112.88 108.12 4.76 1.29e+00 6.01e-01 1.36e+01 angle pdb=" CA GLY B1508 " pdb=" C GLY B1508 " pdb=" O GLY B1508 " ideal model delta sigma weight residual 122.15 117.92 4.23 1.17e+00 7.31e-01 1.31e+01 angle pdb=" N ASP B 889 " pdb=" CA ASP B 889 " pdb=" C ASP B 889 " ideal model delta sigma weight residual 114.39 109.39 5.00 1.45e+00 4.76e-01 1.19e+01 angle pdb=" O LYS B1504 " pdb=" C LYS B1504 " pdb=" N PRO B1505 " ideal model delta sigma weight residual 121.55 119.02 2.53 7.80e-01 1.64e+00 1.05e+01 ... (remaining 18413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7440 17.98 - 35.97: 661 35.97 - 53.95: 117 53.95 - 71.93: 19 71.93 - 89.91: 15 Dihedral angle restraints: 8252 sinusoidal: 3312 harmonic: 4940 Sorted by residual: dihedral pdb=" CA ILE B1409 " pdb=" C ILE B1409 " pdb=" N LEU B1410 " pdb=" CA LEU B1410 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CB GLU B 256 " pdb=" CG GLU B 256 " pdb=" CD GLU B 256 " pdb=" OE1 GLU B 256 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B1653 " pdb=" CD ARG B1653 " pdb=" NE ARG B1653 " pdb=" CZ ARG B1653 " ideal model delta sinusoidal sigma weight residual 90.00 134.42 -44.42 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 8249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1495 0.040 - 0.079: 429 0.079 - 0.119: 157 0.119 - 0.159: 24 0.159 - 0.199: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CA ILE B 890 " pdb=" N ILE B 890 " pdb=" C ILE B 890 " pdb=" CB ILE B 890 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA LEU B1437 " pdb=" N LEU B1437 " pdb=" C LEU B1437 " pdb=" CB LEU B1437 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE B 885 " pdb=" N ILE B 885 " pdb=" C ILE B 885 " pdb=" CB ILE B 885 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 2103 not shown) Planarity restraints: 2371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B1504 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C LYS B1504 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS B1504 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO B1505 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 294 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 295 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 163 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 164 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.025 5.00e-02 4.00e+02 ... (remaining 2368 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1352 2.75 - 3.29: 13157 3.29 - 3.82: 21936 3.82 - 4.36: 26099 4.36 - 4.90: 46055 Nonbonded interactions: 108599 Sorted by model distance: nonbonded pdb=" OH TYR B 125 " pdb=" O GLY B 365 " model vdw 2.211 3.040 nonbonded pdb=" O GLY B1432 " pdb=" OH TYR B1463 " model vdw 2.224 3.040 nonbonded pdb=" O ASN B 602 " pdb=" OG SER B 606 " model vdw 2.248 3.040 nonbonded pdb=" O VAL B 374 " pdb=" OH TYR B 479 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASP B 547 " pdb="ZN ZN B3001 " model vdw 2.277 2.230 ... (remaining 108594 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 ========== 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: 2.440 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.400 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 0.037 13624 Z= 0.155 Angle : 0.485 7.747 18418 Z= 0.282 Chirality : 0.043 0.199 2106 Planarity : 0.003 0.046 2371 Dihedral : 14.351 89.914 5056 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.46 % Allowed : 0.39 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1654 helix: 1.70 (0.21), residues: 650 sheet: 0.58 (0.29), residues: 326 loop : -0.24 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.004 0.001 HIS B 294 PHE 0.020 0.001 PHE B 243 TYR 0.013 0.001 TYR B 581 ARG 0.006 0.000 ARG B 16 Details of bonding type rmsd hydrogen bonds : bond 0.14061 ( 667) hydrogen bonds : angle 6.02767 ( 1902) metal coordination : bond 0.00213 ( 3) covalent geometry : bond 0.00283 (13621) covalent geometry : angle 0.48544 (18418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 254 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: B 920 SER cc_start: 0.8187 (t) cc_final: 0.7779 (p) REVERT: B 1500 MET cc_start: 0.7121 (mmt) cc_final: 0.6771 (mmm) REVERT: B 1526 ILE cc_start: 0.8669 (mp) cc_final: 0.8445 (mm) REVERT: B 1881 ILE cc_start: 0.8014 (mt) cc_final: 0.7729 (tt) outliers start: 7 outliers final: 2 residues processed: 258 average time/residue: 1.1619 time to fit residues: 332.5702 Evaluate side-chains 146 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 1523 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 294 HIS B 602 ASN ** B1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1630 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142706 restraints weight = 17168.359| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.38 r_work: 0.3561 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13624 Z= 0.157 Angle : 0.537 7.077 18418 Z= 0.292 Chirality : 0.045 0.161 2106 Planarity : 0.004 0.048 2371 Dihedral : 4.132 29.722 1782 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.24 % Allowed : 10.34 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1654 helix: 1.70 (0.20), residues: 666 sheet: 0.40 (0.28), residues: 331 loop : -0.23 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 102 HIS 0.004 0.001 HIS B 758 PHE 0.022 0.002 PHE B 504 TYR 0.022 0.002 TYR B1646 ARG 0.005 0.001 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 667) hydrogen bonds : angle 4.64628 ( 1902) metal coordination : bond 0.00344 ( 3) covalent geometry : bond 0.00363 (13621) covalent geometry : angle 0.53739 (18418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.529 Fit side-chains REVERT: B 155 GLU cc_start: 0.7913 (tp30) cc_final: 0.7702 (tp30) REVERT: B 213 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: B 286 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: B 522 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7817 (mt0) REVERT: B 690 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7305 (mptp) REVERT: B 920 SER cc_start: 0.8446 (t) cc_final: 0.7846 (p) REVERT: B 991 TYR cc_start: 0.7568 (t80) cc_final: 0.7098 (t80) REVERT: B 1406 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.6889 (p) REVERT: B 1438 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6978 (tpp) REVERT: B 1465 PHE cc_start: 0.7258 (t80) cc_final: 0.6959 (t80) REVERT: B 1466 MET cc_start: 0.5004 (mmp) cc_final: 0.3126 (pmm) REVERT: B 1741 TYR cc_start: 0.8720 (m-80) cc_final: 0.8513 (m-80) REVERT: B 1881 ILE cc_start: 0.8130 (mt) cc_final: 0.7641 (tt) REVERT: A 31 PHE cc_start: 0.6969 (m-80) cc_final: 0.6657 (m-80) outliers start: 34 outliers final: 11 residues processed: 196 average time/residue: 1.3419 time to fit residues: 293.5495 Evaluate side-chains 155 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1406 THR Chi-restraints excluded: chain B residue 1438 MET Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1710 GLU Chi-restraints excluded: chain B residue 1761 VAL Chi-restraints excluded: chain B residue 1880 THR Chi-restraints excluded: chain A residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 114 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 832 ASN B 924 ASN ** B1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1571 ASN ** B1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1886 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.178009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142613 restraints weight = 17065.799| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.40 r_work: 0.3574 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13624 Z= 0.125 Angle : 0.488 7.602 18418 Z= 0.265 Chirality : 0.044 0.163 2106 Planarity : 0.003 0.049 2371 Dihedral : 3.923 17.641 1778 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.70 % Allowed : 12.64 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1654 helix: 1.85 (0.20), residues: 665 sheet: 0.37 (0.28), residues: 330 loop : -0.24 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.003 0.001 HIS B 758 PHE 0.020 0.001 PHE B 504 TYR 0.018 0.001 TYR B1646 ARG 0.006 0.000 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 667) hydrogen bonds : angle 4.40586 ( 1902) metal coordination : bond 0.00268 ( 3) covalent geometry : bond 0.00290 (13621) covalent geometry : angle 0.48823 (18418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 2.870 Fit side-chains REVERT: B 39 GLU cc_start: 0.7526 (mp0) cc_final: 0.6782 (pp20) REVERT: B 234 GLU cc_start: 0.7455 (tp30) cc_final: 0.7165 (mm-30) REVERT: B 286 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: B 322 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7644 (mpp) REVERT: B 334 LYS cc_start: 0.7994 (mmpt) cc_final: 0.7554 (mtmp) REVERT: B 522 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: B 525 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: B 636 ARG cc_start: 0.8534 (mpt-90) cc_final: 0.8191 (mpt180) REVERT: B 690 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7330 (mptp) REVERT: B 991 TYR cc_start: 0.7688 (t80) cc_final: 0.7217 (t80) REVERT: B 1406 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.6889 (p) REVERT: B 1440 ASN cc_start: 0.5793 (t0) cc_final: 0.5544 (t0) REVERT: B 1465 PHE cc_start: 0.7387 (t80) cc_final: 0.7035 (t80) REVERT: B 1466 MET cc_start: 0.5355 (mmp) cc_final: 0.3233 (pmt) REVERT: B 1493 VAL cc_start: 0.7636 (m) cc_final: 0.7191 (p) REVERT: B 1881 ILE cc_start: 0.8161 (mt) cc_final: 0.7664 (tt) REVERT: A 31 PHE cc_start: 0.7037 (m-80) cc_final: 0.6818 (m-80) outliers start: 41 outliers final: 15 residues processed: 177 average time/residue: 2.0007 time to fit residues: 394.9873 Evaluate side-chains 162 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 926 ILE Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1406 THR Chi-restraints excluded: chain B residue 1480 THR Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1621 GLN Chi-restraints excluded: chain B residue 1626 CYS Chi-restraints excluded: chain B residue 1710 GLU Chi-restraints excluded: chain B residue 1761 VAL Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1880 THR Chi-restraints excluded: chain A residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.0470 chunk 159 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 78 optimal weight: 0.3980 chunk 131 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 118 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 924 ASN ** B1445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145220 restraints weight = 17002.365| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.39 r_work: 0.3613 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13624 Z= 0.094 Angle : 0.450 8.988 18418 Z= 0.244 Chirality : 0.043 0.170 2106 Planarity : 0.003 0.045 2371 Dihedral : 3.707 16.518 1778 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.17 % Allowed : 14.09 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1654 helix: 2.13 (0.20), residues: 658 sheet: 0.38 (0.28), residues: 332 loop : -0.14 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS B 758 PHE 0.020 0.001 PHE B1475 TYR 0.017 0.001 TYR B1426 ARG 0.005 0.000 ARG B 806 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 667) hydrogen bonds : angle 4.15384 ( 1902) metal coordination : bond 0.00122 ( 3) covalent geometry : bond 0.00202 (13621) covalent geometry : angle 0.45037 (18418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 2.414 Fit side-chains REVERT: B 232 VAL cc_start: 0.7601 (p) cc_final: 0.7388 (t) REVERT: B 234 GLU cc_start: 0.7250 (tp30) cc_final: 0.6936 (mm-30) REVERT: B 286 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: B 445 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8023 (tt) REVERT: B 575 GLU cc_start: 0.7512 (mp0) cc_final: 0.7129 (mp0) REVERT: B 636 ARG cc_start: 0.8489 (mpt-90) cc_final: 0.8184 (mpt180) REVERT: B 690 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7182 (mptp) REVERT: B 739 SER cc_start: 0.8813 (p) cc_final: 0.8530 (t) REVERT: B 1406 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.6900 (p) REVERT: B 1440 ASN cc_start: 0.6076 (t0) cc_final: 0.5672 (t0) REVERT: B 1465 PHE cc_start: 0.7361 (t80) cc_final: 0.7080 (t80) REVERT: B 1466 MET cc_start: 0.5294 (mmp) cc_final: 0.3268 (pmt) REVERT: B 1493 VAL cc_start: 0.7422 (m) cc_final: 0.7068 (p) REVERT: B 1881 ILE cc_start: 0.8101 (mt) cc_final: 0.7621 (tt) outliers start: 33 outliers final: 14 residues processed: 189 average time/residue: 1.8968 time to fit residues: 406.2157 Evaluate side-chains 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain B residue 926 ILE Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1406 THR Chi-restraints excluded: chain B residue 1480 THR Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1761 VAL Chi-restraints excluded: chain B residue 1837 VAL Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain A residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5379 > 50: distance: 52 - 153: 18.547 distance: 55 - 150: 9.001 distance: 64 - 134: 23.103 distance: 67 - 131: 15.470 distance: 77 - 121: 21.333 distance: 79 - 85: 27.514 distance: 80 - 118: 3.103 distance: 85 - 86: 12.651 distance: 86 - 87: 12.434 distance: 86 - 89: 19.844 distance: 87 - 88: 28.020 distance: 87 - 91: 20.689 distance: 91 - 92: 15.169 distance: 92 - 93: 6.089 distance: 92 - 95: 7.405 distance: 93 - 94: 18.728 distance: 93 - 102: 12.352 distance: 95 - 96: 16.760 distance: 96 - 97: 11.025 distance: 96 - 98: 9.929 distance: 97 - 99: 6.244 distance: 102 - 103: 23.977 distance: 103 - 104: 7.414 distance: 103 - 106: 23.798 distance: 104 - 105: 10.602 distance: 104 - 109: 25.804 distance: 106 - 107: 9.933 distance: 106 - 108: 14.113 distance: 109 - 110: 33.468 distance: 110 - 111: 12.490 distance: 110 - 113: 33.148 distance: 111 - 112: 13.087 distance: 111 - 118: 19.938 distance: 113 - 114: 36.274 distance: 114 - 115: 16.457 distance: 115 - 116: 10.979 distance: 118 - 119: 5.235 distance: 119 - 120: 12.009 distance: 119 - 122: 19.536 distance: 120 - 121: 25.793 distance: 120 - 127: 19.241 distance: 122 - 123: 15.258 distance: 123 - 124: 15.213 distance: 124 - 125: 19.881 distance: 124 - 126: 8.538 distance: 127 - 128: 9.484 distance: 127 - 213: 26.668 distance: 128 - 129: 13.670 distance: 129 - 130: 10.123 distance: 129 - 131: 17.775 distance: 130 - 210: 11.225 distance: 131 - 132: 8.258 distance: 132 - 133: 6.705 distance: 132 - 135: 14.449 distance: 133 - 134: 4.016 distance: 133 - 139: 5.744 distance: 135 - 136: 8.676 distance: 136 - 137: 16.516 distance: 136 - 138: 10.430 distance: 139 - 140: 8.509 distance: 139 - 198: 16.917 distance: 140 - 141: 9.252 distance: 140 - 143: 36.587 distance: 141 - 142: 7.070 distance: 141 - 150: 20.074 distance: 142 - 195: 30.612 distance: 143 - 144: 3.967 distance: 144 - 145: 18.521 distance: 144 - 146: 14.805 distance: 145 - 147: 19.795 distance: 146 - 148: 18.504 distance: 147 - 149: 15.359 distance: 148 - 149: 14.501 distance: 150 - 151: 6.692 distance: 151 - 152: 11.606 distance: 151 - 154: 7.602 distance: 152 - 153: 4.639 distance: 152 - 157: 8.846 distance: 154 - 155: 9.299 distance: 154 - 156: 6.854 distance: 157 - 158: 15.900 distance: 157 - 183: 9.474 distance: 158 - 159: 5.308 distance: 158 - 161: 18.711 distance: 159 - 160: 8.771 distance: 159 - 163: 4.993 distance: 160 - 180: 11.121 distance: 161 - 162: 17.825