Starting phenix.real_space_refine on Wed Jan 14 01:01:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e04_27813/01_2026/8e04_27813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e04_27813/01_2026/8e04_27813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e04_27813/01_2026/8e04_27813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e04_27813/01_2026/8e04_27813.map" model { file = "/net/cci-nas-00/data/ceres_data/8e04_27813/01_2026/8e04_27813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e04_27813/01_2026/8e04_27813.cif" } resolution = 3.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 P 2 5.49 5 S 74 5.16 5 C 6825 2.51 5 N 1818 2.21 5 O 1972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10691 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10663 Classifications: {'peptide': 1343} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1272} Chain breaks: 16 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.76, per 1000 atoms: 0.26 Number of scatterers: 10691 At special positions: 0 Unit cell: (84.68, 103.24, 150.8, 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) S 74 16.00 P 2 15.00 O 1972 8.00 N 1818 7.00 C 6825 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: 0.88 Conformation dependent library (CDL) restraints added in 449.1 milliseconds 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 35.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.818A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.679A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 490 through 494 removed outlier: 3.512A pdb=" N LYS A 493 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.609A pdb=" N CYS A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 729 through 747 removed outlier: 3.806A pdb=" N VAL A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TRP A 739 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 769 through 783 Processing helix chain 'A' and resid 797 through 799 No H-bonds generated for 'chain 'A' and resid 797 through 799' Processing helix chain 'A' and resid 811 through 826 Processing helix chain 'A' and resid 844 through 865 Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 889 through 903 Processing helix chain 'A' and resid 923 through 936 Processing helix chain 'A' and resid 951 through 958 Processing helix chain 'A' and resid 959 through 962 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 967 through 978 Processing helix chain 'A' and resid 992 through 995 Processing helix chain 'A' and resid 1026 through 1043 Processing helix chain 'A' and resid 1128 through 1144 removed outlier: 3.506A pdb=" N THR A1134 " --> pdb=" O MET A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.505A pdb=" N ALA A1150 " --> pdb=" O ALA A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1198 Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1228 through 1232 Processing helix chain 'A' and resid 1234 through 1236 No H-bonds generated for 'chain 'A' and resid 1234 through 1236' Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1287 through 1312 Processing helix chain 'A' and resid 1341 through 1346 removed outlier: 3.522A pdb=" N VAL A1345 " --> pdb=" O SER A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1380 Processing helix chain 'A' and resid 1388 through 1390 No H-bonds generated for 'chain 'A' and resid 1388 through 1390' Processing helix chain 'A' and resid 1442 through 1460 removed outlier: 4.031A pdb=" N ASP A1446 " --> pdb=" O ASP A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1479 Processing helix chain 'A' and resid 1486 through 1491 Processing helix chain 'A' and resid 1492 through 1503 Processing helix chain 'A' and resid 1506 through 1510 Processing helix chain 'A' and resid 1512 through 1521 Processing helix chain 'A' and resid 1522 through 1527 removed outlier: 3.831A pdb=" N ALA A1526 " --> pdb=" O ASP A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1559 Processing helix chain 'A' and resid 1670 through 1678 Processing helix chain 'A' and resid 1685 through 1689 Processing helix chain 'A' and resid 1950 through 1957 removed outlier: 3.507A pdb=" N LEU A1953 " --> pdb=" O ALA A1950 " (cutoff:3.500A) Proline residue: A1955 - end of helix Processing helix chain 'A' and resid 1990 through 2007 removed outlier: 3.717A pdb=" N TYR A2001 " --> pdb=" O PHE A1997 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A2004 " --> pdb=" O SER A2000 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 384 through 386 removed outlier: 6.404A pdb=" N LEU A 409 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.946A pdb=" N LEU A 553 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 634 through 636 removed outlier: 3.517A pdb=" N ARG A 841 " --> pdb=" O CYS A 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 673 through 681 removed outlier: 7.412A pdb=" N MET A 639 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TRP A 698 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET A 641 " --> pdb=" O TRP A 698 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 700 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 643 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N LEU A 719 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 640 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL A 721 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 642 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 723 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 644 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ASN A 725 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 948 through 950 Processing sheet with id=AA6, first strand: chain 'A' and resid 1080 through 1086 removed outlier: 6.379A pdb=" N GLN A1015 " --> pdb=" O PRO A1164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1203 Processing sheet with id=AA8, first strand: chain 'A' and resid 1238 through 1239 removed outlier: 6.602A pdb=" N ILE A1257 " --> pdb=" O LEU A1248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1238 through 1239 removed outlier: 6.946A pdb=" N CYS A1331 " --> pdb=" O ILE A1325 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A1325 " --> pdb=" O CYS A1331 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A1333 " --> pdb=" O ILE A1323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1392 through 1394 Processing sheet with id=AB2, first strand: chain 'A' and resid 1528 through 1536 removed outlier: 6.455A pdb=" N PHE A1528 " --> pdb=" O ARG A1987 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG A1987 " --> pdb=" O PHE A1528 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A1530 " --> pdb=" O VAL A1985 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TRP A1981 " --> pdb=" O CYS A1534 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1969 " --> pdb=" O VAL A1965 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU A1975 " --> pdb=" O LEU A1959 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A1959 " --> pdb=" O GLU A1975 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1539 through 1542 removed outlier: 3.740A pdb=" N VAL A1550 " --> pdb=" O VAL A1565 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR A1562 " --> pdb=" O ARG A1576 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A1574 " --> pdb=" O VAL A1564 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1584 through 1590 removed outlier: 6.696A pdb=" N ALA A1597 " --> pdb=" O SER A1585 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN A1587 " --> pdb=" O TRP A1595 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP A1595 " --> pdb=" O GLN A1587 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN A1589 " --> pdb=" O SER A1593 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A1593 " --> pdb=" O GLN A1589 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A1602 " --> pdb=" O THR A1598 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A1619 " --> pdb=" O ILE A1605 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1627 through 1633 Processing sheet with id=AB6, first strand: chain 'A' and resid 1627 through 1633 Processing sheet with id=AB7, first strand: chain 'A' and resid 1696 through 1699 removed outlier: 3.885A pdb=" N ARG A1725 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP A1717 " --> pdb=" O ILE A1723 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A1723 " --> pdb=" O ASP A1717 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1736 through 1741 removed outlier: 4.362A pdb=" N SER A1738 " --> pdb=" O LEU A1754 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER A1760 " --> pdb=" O ASP A1755 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS A1765 " --> pdb=" O LEU A1771 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A1771 " --> pdb=" O HIS A1765 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1786 through 1788 removed outlier: 6.845A pdb=" N VAL A1930 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A1947 " --> pdb=" O VAL A1928 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL A1928 " --> pdb=" O VAL A1947 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1776 1.31 - 1.44: 2798 1.44 - 1.56: 6228 1.56 - 1.69: 5 1.69 - 1.82: 108 Bond restraints: 10915 Sorted by residual: bond pdb=" C LEU A1754 " pdb=" O LEU A1754 " ideal model delta sigma weight residual 1.233 1.193 0.040 1.31e-02 5.83e+03 9.51e+00 bond pdb=" CA ALA A1946 " pdb=" CB ALA A1946 " ideal model delta sigma weight residual 1.535 1.486 0.049 1.58e-02 4.01e+03 9.50e+00 bond pdb=" N LEU A1754 " pdb=" CA LEU A1754 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.22e-02 6.72e+03 8.78e+00 bond pdb=" C ILE A1945 " pdb=" O ILE A1945 " ideal model delta sigma weight residual 1.237 1.205 0.033 1.17e-02 7.31e+03 7.74e+00 bond pdb=" N GLN A1688 " pdb=" CA GLN A1688 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.64e+00 ... (remaining 10910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 14367 2.02 - 4.04: 343 4.04 - 6.05: 71 6.05 - 8.07: 10 8.07 - 10.09: 1 Bond angle restraints: 14792 Sorted by residual: angle pdb=" CA ASP A1755 " pdb=" C ASP A1755 " pdb=" O ASP A1755 " ideal model delta sigma weight residual 121.51 114.02 7.49 1.12e+00 7.97e-01 4.48e+01 angle pdb=" C TRP A1503 " pdb=" CA TRP A1503 " pdb=" CB TRP A1503 " ideal model delta sigma weight residual 110.72 100.63 10.09 1.77e+00 3.19e-01 3.25e+01 angle pdb=" N VAL A1944 " pdb=" CA VAL A1944 " pdb=" CB VAL A1944 " ideal model delta sigma weight residual 112.06 107.15 4.91 9.70e-01 1.06e+00 2.56e+01 angle pdb=" CA LEU A1754 " pdb=" C LEU A1754 " pdb=" O LEU A1754 " ideal model delta sigma weight residual 121.88 115.43 6.45 1.30e+00 5.92e-01 2.46e+01 angle pdb=" CA VAL A1944 " pdb=" C VAL A1944 " pdb=" O VAL A1944 " ideal model delta sigma weight residual 121.70 116.87 4.83 1.06e+00 8.90e-01 2.07e+01 ... (remaining 14787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 6089 18.22 - 36.43: 404 36.43 - 54.65: 80 54.65 - 72.86: 20 72.86 - 91.08: 10 Dihedral angle restraints: 6603 sinusoidal: 2693 harmonic: 3910 Sorted by residual: dihedral pdb=" C TRP A1503 " pdb=" N TRP A1503 " pdb=" CA TRP A1503 " pdb=" CB TRP A1503 " ideal model delta harmonic sigma weight residual -122.60 -109.39 -13.21 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C GLN A1491 " pdb=" N GLN A1491 " pdb=" CA GLN A1491 " pdb=" CB GLN A1491 " ideal model delta harmonic sigma weight residual -122.60 -133.17 10.57 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C THR A1505 " pdb=" N THR A1505 " pdb=" CA THR A1505 " pdb=" CB THR A1505 " ideal model delta harmonic sigma weight residual -122.00 -130.87 8.87 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 6600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1424 0.063 - 0.126: 217 0.126 - 0.189: 24 0.189 - 0.252: 5 0.252 - 0.315: 3 Chirality restraints: 1673 Sorted by residual: chirality pdb=" CA TRP A1503 " pdb=" N TRP A1503 " pdb=" C TRP A1503 " pdb=" CB TRP A1503 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA GLN A1491 " pdb=" N GLN A1491 " pdb=" C GLN A1491 " pdb=" CB GLN A1491 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ASP A1504 " pdb=" N ASP A1504 " pdb=" C ASP A1504 " pdb=" CB ASP A1504 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1670 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1492 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C PHE A1492 " -0.069 2.00e-02 2.50e+03 pdb=" O PHE A1492 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A1493 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1753 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C CYS A1753 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS A1753 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A1754 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 542 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 543 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.046 5.00e-02 4.00e+02 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 498 2.72 - 3.27: 10674 3.27 - 3.81: 17218 3.81 - 4.36: 21394 4.36 - 4.90: 36369 Nonbonded interactions: 86153 Sorted by model distance: nonbonded pdb=" O VAL A 455 " pdb=" OD1 ASP A 456 " model vdw 2.179 3.040 nonbonded pdb=" OG SER A 547 " pdb=" O LEU A 569 " model vdw 2.256 3.040 nonbonded pdb=" N GLU A 590 " pdb=" OE1 GLU A 590 " model vdw 2.260 3.120 nonbonded pdb=" O ASN A1391 " pdb=" OG SER A1408 " model vdw 2.282 3.040 nonbonded pdb=" NZ LYS A1365 " pdb=" O VAL A1399 " model vdw 2.293 3.120 ... (remaining 86148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.010 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 : 0.004 0.053 10915 Z= 0.224 Angle : 0.785 10.088 14792 Z= 0.455 Chirality : 0.049 0.315 1673 Planarity : 0.005 0.084 1886 Dihedral : 13.454 91.077 4057 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.41 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1309 helix: 1.34 (0.29), residues: 354 sheet: -1.06 (0.27), residues: 307 loop : -0.19 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1481 TYR 0.017 0.002 TYR A 577 PHE 0.037 0.002 PHE A 419 TRP 0.010 0.001 TRP A1028 HIS 0.010 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00430 (10915) covalent geometry : angle 0.78547 (14792) hydrogen bonds : bond 0.14946 ( 462) hydrogen bonds : angle 6.48226 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 395 LEU cc_start: 0.8034 (tp) cc_final: 0.7688 (tt) REVERT: A 1562 TYR cc_start: 0.7880 (p90) cc_final: 0.7669 (p90) REVERT: A 1786 MET cc_start: 0.7251 (mtt) cc_final: 0.7048 (mtp) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.0978 time to fit residues: 19.9979 Evaluate side-chains 106 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 ASN A1364 GLN A1391 ASN A1688 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.163108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127876 restraints weight = 18287.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126590 restraints weight = 15507.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.128261 restraints weight = 15802.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129218 restraints weight = 11029.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129654 restraints weight = 10216.607| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10915 Z= 0.131 Angle : 0.588 9.242 14792 Z= 0.296 Chirality : 0.044 0.142 1673 Planarity : 0.005 0.065 1886 Dihedral : 4.524 43.881 1447 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.01 % Allowed : 7.67 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.24), residues: 1309 helix: 1.57 (0.29), residues: 363 sheet: -0.81 (0.28), residues: 296 loop : -0.14 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 789 TYR 0.015 0.001 TYR A1707 PHE 0.022 0.002 PHE A 974 TRP 0.014 0.001 TRP A1986 HIS 0.004 0.001 HIS A1360 Details of bonding type rmsd covalent geometry : bond 0.00303 (10915) covalent geometry : angle 0.58835 (14792) hydrogen bonds : bond 0.03563 ( 462) hydrogen bonds : angle 5.26985 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.7129 (mp) cc_final: 0.6821 (tp) REVERT: A 456 ASP cc_start: 0.7445 (m-30) cc_final: 0.7060 (p0) REVERT: A 893 LEU cc_start: 0.8721 (pp) cc_final: 0.8452 (tt) REVERT: A 1562 TYR cc_start: 0.7985 (p90) cc_final: 0.7754 (p90) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.0961 time to fit residues: 18.8648 Evaluate side-chains 111 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1737 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 104 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A 868 GLN A1391 ASN A1566 ASN A1688 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.162000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127724 restraints weight = 18298.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126372 restraints weight = 16538.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.127811 restraints weight = 16317.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130807 restraints weight = 11584.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131003 restraints weight = 8863.837| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10915 Z= 0.133 Angle : 0.560 9.035 14792 Z= 0.280 Chirality : 0.044 0.154 1673 Planarity : 0.004 0.055 1886 Dihedral : 4.180 25.619 1445 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.35 % Allowed : 8.68 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1309 helix: 1.59 (0.29), residues: 364 sheet: -0.90 (0.28), residues: 306 loop : -0.03 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 783 TYR 0.017 0.001 TYR A1455 PHE 0.018 0.002 PHE A1974 TRP 0.015 0.001 TRP A1503 HIS 0.003 0.001 HIS A1956 Details of bonding type rmsd covalent geometry : bond 0.00308 (10915) covalent geometry : angle 0.55953 (14792) hydrogen bonds : bond 0.03399 ( 462) hydrogen bonds : angle 5.03474 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.7155 (mp) cc_final: 0.6830 (tp) REVERT: A 495 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7737 (m) REVERT: A 893 LEU cc_start: 0.8684 (pp) cc_final: 0.8453 (tt) REVERT: A 950 ARG cc_start: 0.7581 (tpt-90) cc_final: 0.7316 (ptp-110) REVERT: A 1562 TYR cc_start: 0.8029 (p90) cc_final: 0.7780 (p90) REVERT: A 1688 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7544 (tp40) outliers start: 16 outliers final: 9 residues processed: 131 average time/residue: 0.0907 time to fit residues: 17.8519 Evaluate side-chains 118 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1688 GLN Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1737 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 52 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 53 optimal weight: 0.0770 chunk 112 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127139 restraints weight = 18819.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127515 restraints weight = 17398.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128853 restraints weight = 16863.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129432 restraints weight = 10820.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130296 restraints weight = 10210.631| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10915 Z= 0.172 Angle : 0.589 9.233 14792 Z= 0.293 Chirality : 0.044 0.172 1673 Planarity : 0.004 0.048 1886 Dihedral : 4.244 26.328 1445 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.60 % Allowed : 9.27 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1309 helix: 1.56 (0.29), residues: 363 sheet: -0.96 (0.28), residues: 304 loop : -0.06 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1687 TYR 0.018 0.001 TYR A1764 PHE 0.021 0.002 PHE A 974 TRP 0.019 0.001 TRP A1503 HIS 0.005 0.001 HIS A1956 Details of bonding type rmsd covalent geometry : bond 0.00409 (10915) covalent geometry : angle 0.58932 (14792) hydrogen bonds : bond 0.03510 ( 462) hydrogen bonds : angle 5.03077 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.7295 (mp) cc_final: 0.7028 (tp) REVERT: A 456 ASP cc_start: 0.7270 (m-30) cc_final: 0.7044 (p0) REVERT: A 495 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7415 (m) REVERT: A 893 LEU cc_start: 0.8659 (pp) cc_final: 0.8387 (tt) REVERT: A 950 ARG cc_start: 0.7643 (tpt-90) cc_final: 0.7368 (ptp-110) REVERT: A 1447 MET cc_start: 0.8750 (mmm) cc_final: 0.8314 (mmt) REVERT: A 1562 TYR cc_start: 0.8057 (p90) cc_final: 0.7808 (p90) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.0819 time to fit residues: 15.9452 Evaluate side-chains 121 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1973 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 76 optimal weight: 0.0570 chunk 95 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1391 ASN A1956 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.163850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128171 restraints weight = 18298.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126784 restraints weight = 15167.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.128488 restraints weight = 15879.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129487 restraints weight = 11009.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130011 restraints weight = 10221.618| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10915 Z= 0.104 Angle : 0.571 11.740 14792 Z= 0.272 Chirality : 0.043 0.166 1673 Planarity : 0.004 0.042 1886 Dihedral : 4.062 26.048 1445 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.60 % Allowed : 9.95 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1309 helix: 1.67 (0.29), residues: 363 sheet: -0.85 (0.28), residues: 308 loop : 0.03 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.014 0.001 TYR A1764 PHE 0.016 0.001 PHE A1076 TRP 0.014 0.001 TRP A1503 HIS 0.002 0.001 HIS A1136 Details of bonding type rmsd covalent geometry : bond 0.00238 (10915) covalent geometry : angle 0.57138 (14792) hydrogen bonds : bond 0.03095 ( 462) hydrogen bonds : angle 4.89651 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 ASP cc_start: 0.7400 (m-30) cc_final: 0.7108 (p0) REVERT: A 495 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7561 (m) REVERT: A 503 ASP cc_start: 0.7659 (t0) cc_final: 0.7158 (t70) REVERT: A 893 LEU cc_start: 0.8678 (pp) cc_final: 0.8433 (tt) REVERT: A 950 ARG cc_start: 0.7693 (tpt-90) cc_final: 0.7297 (ptp-110) REVERT: A 1447 MET cc_start: 0.8815 (mmm) cc_final: 0.8466 (mmt) REVERT: A 1562 TYR cc_start: 0.7960 (p90) cc_final: 0.7524 (p90) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 0.0907 time to fit residues: 17.8913 Evaluate side-chains 121 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1572 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1615 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1973 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1369 GLN A1391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126859 restraints weight = 18692.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126086 restraints weight = 15661.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127626 restraints weight = 16738.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128341 restraints weight = 11395.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.128697 restraints weight = 10532.032| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10915 Z= 0.127 Angle : 0.586 11.543 14792 Z= 0.278 Chirality : 0.044 0.188 1673 Planarity : 0.004 0.039 1886 Dihedral : 4.043 25.693 1445 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.77 % Allowed : 10.29 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1309 helix: 1.73 (0.29), residues: 363 sheet: -0.91 (0.28), residues: 311 loop : 0.09 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1943 TYR 0.015 0.001 TYR A 577 PHE 0.017 0.002 PHE A 974 TRP 0.020 0.001 TRP A1503 HIS 0.003 0.001 HIS A1136 Details of bonding type rmsd covalent geometry : bond 0.00303 (10915) covalent geometry : angle 0.58637 (14792) hydrogen bonds : bond 0.03095 ( 462) hydrogen bonds : angle 4.81475 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7451 (m) REVERT: A 893 LEU cc_start: 0.8684 (pp) cc_final: 0.8454 (tt) REVERT: A 950 ARG cc_start: 0.7662 (tpt-90) cc_final: 0.7335 (ptp-110) REVERT: A 1376 TYR cc_start: 0.9014 (t80) cc_final: 0.8811 (t80) REVERT: A 1447 MET cc_start: 0.8832 (mmm) cc_final: 0.8497 (mmt) REVERT: A 1562 TYR cc_start: 0.8036 (p90) cc_final: 0.7663 (p90) outliers start: 21 outliers final: 18 residues processed: 129 average time/residue: 0.0872 time to fit residues: 17.0271 Evaluate side-chains 125 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1615 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1973 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 104 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 ASN ** A1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.127222 restraints weight = 18630.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126066 restraints weight = 15928.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127629 restraints weight = 16153.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128607 restraints weight = 10946.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129171 restraints weight = 10065.529| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10915 Z= 0.123 Angle : 0.594 13.004 14792 Z= 0.281 Chirality : 0.044 0.238 1673 Planarity : 0.004 0.056 1886 Dihedral : 4.056 25.557 1445 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.85 % Allowed : 11.05 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1309 helix: 1.84 (0.29), residues: 363 sheet: -0.90 (0.28), residues: 304 loop : 0.07 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.024 0.001 TYR A1691 PHE 0.016 0.001 PHE A 974 TRP 0.020 0.001 TRP A1503 HIS 0.003 0.001 HIS A1136 Details of bonding type rmsd covalent geometry : bond 0.00291 (10915) covalent geometry : angle 0.59377 (14792) hydrogen bonds : bond 0.03054 ( 462) hydrogen bonds : angle 4.78838 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 LEU cc_start: 0.8746 (mm) cc_final: 0.8391 (mm) REVERT: A 576 LEU cc_start: 0.9071 (tp) cc_final: 0.8798 (mt) REVERT: A 893 LEU cc_start: 0.8789 (pp) cc_final: 0.8410 (tt) REVERT: A 950 ARG cc_start: 0.7749 (tpt-90) cc_final: 0.7346 (ptp-110) REVERT: A 1376 TYR cc_start: 0.8999 (t80) cc_final: 0.8757 (t80) REVERT: A 1447 MET cc_start: 0.8816 (mmm) cc_final: 0.8490 (mmt) REVERT: A 1562 TYR cc_start: 0.8001 (p90) cc_final: 0.7688 (p90) outliers start: 22 outliers final: 19 residues processed: 126 average time/residue: 0.1021 time to fit residues: 18.7888 Evaluate side-chains 125 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1572 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1615 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1973 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 14 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.161710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125827 restraints weight = 18552.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124365 restraints weight = 15744.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125996 restraints weight = 15919.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126881 restraints weight = 11030.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127350 restraints weight = 10370.079| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10915 Z= 0.143 Angle : 0.617 13.718 14792 Z= 0.292 Chirality : 0.044 0.220 1673 Planarity : 0.004 0.038 1886 Dihedral : 4.087 25.674 1445 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.02 % Allowed : 11.30 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.24), residues: 1309 helix: 1.69 (0.28), residues: 363 sheet: -1.01 (0.28), residues: 302 loop : 0.01 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.026 0.002 TYR A1691 PHE 0.023 0.002 PHE A 545 TRP 0.025 0.001 TRP A1503 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00338 (10915) covalent geometry : angle 0.61695 (14792) hydrogen bonds : bond 0.03173 ( 462) hydrogen bonds : angle 4.82309 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 456 ASP cc_start: 0.7989 (t0) cc_final: 0.7672 (p0) REVERT: A 479 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7640 (mmm160) REVERT: A 570 LEU cc_start: 0.8732 (mm) cc_final: 0.8250 (mm) REVERT: A 698 TRP cc_start: 0.8801 (m-10) cc_final: 0.8578 (m-10) REVERT: A 893 LEU cc_start: 0.8801 (pp) cc_final: 0.8436 (tt) REVERT: A 950 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7343 (ptp-110) REVERT: A 1376 TYR cc_start: 0.8970 (t80) cc_final: 0.8736 (t80) REVERT: A 1447 MET cc_start: 0.8783 (mmm) cc_final: 0.8461 (mmt) REVERT: A 1562 TYR cc_start: 0.8027 (p90) cc_final: 0.7710 (p90) REVERT: A 1735 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6157 (ttm) outliers start: 24 outliers final: 20 residues processed: 125 average time/residue: 0.0996 time to fit residues: 18.4980 Evaluate side-chains 124 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1572 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1615 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1973 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126727 restraints weight = 18460.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126036 restraints weight = 15530.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127734 restraints weight = 16207.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128555 restraints weight = 10525.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129195 restraints weight = 9877.359| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10915 Z= 0.127 Angle : 0.608 13.794 14792 Z= 0.292 Chirality : 0.044 0.156 1673 Planarity : 0.004 0.039 1886 Dihedral : 4.027 25.659 1445 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.85 % Allowed : 11.72 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1309 helix: 1.66 (0.28), residues: 363 sheet: -1.01 (0.29), residues: 296 loop : -0.04 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 413 TYR 0.027 0.001 TYR A1691 PHE 0.015 0.001 PHE A 974 TRP 0.023 0.001 TRP A1503 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00302 (10915) covalent geometry : angle 0.60805 (14792) hydrogen bonds : bond 0.03113 ( 462) hydrogen bonds : angle 4.81489 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 456 ASP cc_start: 0.7843 (t0) cc_final: 0.7581 (p0) REVERT: A 479 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7461 (mmm160) REVERT: A 503 ASP cc_start: 0.7727 (t0) cc_final: 0.7046 (t70) REVERT: A 570 LEU cc_start: 0.8800 (mm) cc_final: 0.8391 (mm) REVERT: A 698 TRP cc_start: 0.8776 (m-10) cc_final: 0.8555 (m-10) REVERT: A 893 LEU cc_start: 0.8783 (pp) cc_final: 0.8407 (tt) REVERT: A 950 ARG cc_start: 0.7794 (tpt-90) cc_final: 0.7315 (ptp-110) REVERT: A 1447 MET cc_start: 0.8775 (mmm) cc_final: 0.8478 (mmt) REVERT: A 1562 TYR cc_start: 0.8029 (p90) cc_final: 0.7695 (p90) REVERT: A 1735 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6111 (ttm) outliers start: 22 outliers final: 19 residues processed: 119 average time/residue: 0.0955 time to fit residues: 17.0607 Evaluate side-chains 120 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1496 GLN Chi-restraints excluded: chain A residue 1572 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1973 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 66 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1369 GLN A1496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.161330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126053 restraints weight = 18448.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123939 restraints weight = 15864.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125641 restraints weight = 16393.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126528 restraints weight = 11302.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127072 restraints weight = 10499.387| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10915 Z= 0.150 Angle : 0.632 13.761 14792 Z= 0.302 Chirality : 0.044 0.161 1673 Planarity : 0.004 0.039 1886 Dihedral : 4.062 25.899 1445 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.11 % Allowed : 11.64 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1309 helix: 1.73 (0.28), residues: 357 sheet: -1.07 (0.28), residues: 302 loop : -0.03 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 413 TYR 0.029 0.002 TYR A1691 PHE 0.018 0.002 PHE A 974 TRP 0.029 0.001 TRP A1503 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00360 (10915) covalent geometry : angle 0.63231 (14792) hydrogen bonds : bond 0.03224 ( 462) hydrogen bonds : angle 4.83677 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 456 ASP cc_start: 0.7961 (t0) cc_final: 0.7675 (p0) REVERT: A 479 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7571 (mmm160) REVERT: A 503 ASP cc_start: 0.7824 (t0) cc_final: 0.7067 (t70) REVERT: A 570 LEU cc_start: 0.8855 (mm) cc_final: 0.8641 (mm) REVERT: A 893 LEU cc_start: 0.8799 (pp) cc_final: 0.8454 (tt) REVERT: A 950 ARG cc_start: 0.7999 (tpt-90) cc_final: 0.7586 (ptp-110) REVERT: A 1369 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8416 (mp10) REVERT: A 1447 MET cc_start: 0.8777 (mmm) cc_final: 0.8458 (mmt) REVERT: A 1562 TYR cc_start: 0.8070 (p90) cc_final: 0.7806 (p90) REVERT: A 1735 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6136 (ttm) outliers start: 25 outliers final: 19 residues processed: 124 average time/residue: 0.0908 time to fit residues: 17.0055 Evaluate side-chains 121 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1369 GLN Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1572 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1615 ASN Chi-restraints excluded: chain A residue 1652 VAL Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1735 MET Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1973 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1369 GLN ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.161038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126151 restraints weight = 18502.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125163 restraints weight = 15005.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126488 restraints weight = 16772.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127232 restraints weight = 10893.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127536 restraints weight = 9985.152| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 10915 Z= 0.223 Angle : 0.964 59.200 14792 Z= 0.523 Chirality : 0.045 0.337 1673 Planarity : 0.004 0.039 1886 Dihedral : 4.071 25.899 1445 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.94 % Allowed : 12.06 % Favored : 86.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1309 helix: 1.73 (0.29), residues: 357 sheet: -1.07 (0.28), residues: 302 loop : -0.03 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 413 TYR 0.023 0.002 TYR A1691 PHE 0.018 0.002 PHE A 963 TRP 0.026 0.001 TRP A1503 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00486 (10915) covalent geometry : angle 0.96363 (14792) hydrogen bonds : bond 0.03227 ( 462) hydrogen bonds : angle 4.84021 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1535.57 seconds wall clock time: 27 minutes 29.98 seconds (1649.98 seconds total)