Starting phenix.real_space_refine on Fri Jul 3 15:54:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1v_66467/07_2026/9x1v_66467_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1v_66467/07_2026/9x1v_66467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x1v_66467/07_2026/9x1v_66467_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1v_66467/07_2026/9x1v_66467_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x1v_66467/07_2026/9x1v_66467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1v_66467/07_2026/9x1v_66467.map" } resolution = 2.72 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 9236 2.51 5 N 2451 2.21 5 O 2629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14417 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1657, 13020 Classifications: {'peptide': 1657} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 88, 'TRANS': 1568} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 437 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "C" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 320 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 320 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 320 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Time building chain proxies: 2.71, per 1000 atoms: 0.19 Number of scatterers: 14417 At special positions: 0 Unit cell: (116.8, 149.65, 102.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 2629 8.00 N 2451 7.00 C 9236 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: 1.07 Conformation dependent library (CDL) restraints added in 670.0 milliseconds 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3482 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 10 sheets defined 61.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.705A pdb=" N LEU A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.609A pdb=" N TRP A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.742A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 106' Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.992A pdb=" N ARG A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 Processing helix chain 'A' and resid 176 through 203 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 249 removed outlier: 4.625A pdb=" N PHE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.948A pdb=" N PHE A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 280 through 290 removed outlier: 4.152A pdb=" N VAL A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 318 through 346 Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.854A pdb=" N LYS A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.573A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.977A pdb=" N VAL A 415 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 465 Proline residue: A 461 - end of helix Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 513 through 516 Processing helix chain 'A' and resid 525 through 542 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.780A pdb=" N PHE A 558 " --> pdb=" O CYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 627 through 646 removed outlier: 3.926A pdb=" N ILE A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 688 Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 738 through 756 Processing helix chain 'A' and resid 761 through 779 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.642A pdb=" N ILE A 784 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 805 through 813 Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 819 through 835 removed outlier: 4.471A pdb=" N PHE A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.558A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 877 through 889 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 903 through 916 Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 932 through 947 removed outlier: 3.793A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 957 Processing helix chain 'A' and resid 962 through 979 Processing helix chain 'A' and resid 986 through 991 removed outlier: 4.016A pdb=" N GLU A 991 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1081 through 1100 removed outlier: 3.604A pdb=" N ARG A1100 " --> pdb=" O TRP A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1118 Processing helix chain 'A' and resid 1151 through 1157 removed outlier: 3.639A pdb=" N TRP A1157 " --> pdb=" O ILE A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1196 Processing helix chain 'A' and resid 1210 through 1214 Processing helix chain 'A' and resid 1255 through 1277 removed outlier: 3.505A pdb=" N SER A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1295 removed outlier: 3.959A pdb=" N ARG A1294 " --> pdb=" O ASN A1291 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A1295 " --> pdb=" O LEU A1292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1291 through 1295' Processing helix chain 'A' and resid 1296 through 1303 Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 4.002A pdb=" N VAL A1308 " --> pdb=" O PRO A1304 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1335 Processing helix chain 'A' and resid 1338 through 1348 Processing helix chain 'A' and resid 1350 through 1356 Processing helix chain 'A' and resid 1359 through 1367 Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1371 through 1382 removed outlier: 3.588A pdb=" N LEU A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1385 No H-bonds generated for 'chain 'A' and resid 1383 through 1385' Processing helix chain 'A' and resid 1386 through 1395 Processing helix chain 'A' and resid 1396 through 1397 No H-bonds generated for 'chain 'A' and resid 1396 through 1397' Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.901A pdb=" N TYR A1401 " --> pdb=" O ASN A1398 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A1403 " --> pdb=" O LYS A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1407 No H-bonds generated for 'chain 'A' and resid 1405 through 1407' Processing helix chain 'A' and resid 1408 through 1416 Processing helix chain 'A' and resid 1447 through 1465 removed outlier: 4.079A pdb=" N ASN A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN A1453 " --> pdb=" O LYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1485 Processing helix chain 'A' and resid 1499 through 1509 Processing helix chain 'A' and resid 1512 through 1517 Processing helix chain 'A' and resid 1519 through 1525 Processing helix chain 'A' and resid 1589 through 1594 removed outlier: 3.778A pdb=" N ILE A1593 " --> pdb=" O LEU A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1616 Processing helix chain 'A' and resid 1622 through 1641 Processing helix chain 'A' and resid 1681 through 1687 removed outlier: 3.542A pdb=" N ALA A1685 " --> pdb=" O CYS A1681 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1686 " --> pdb=" O PRO A1682 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A1687 " --> pdb=" O SER A1683 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1681 through 1687' Processing helix chain 'A' and resid 1692 through 1698 Processing helix chain 'A' and resid 1701 through 1709 Processing helix chain 'B' and resid 128 through 167 Processing helix chain 'C' and resid 128 through 166 Processing helix chain 'D' and resid 128 through 166 Processing helix chain 'E' and resid 128 through 166 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.503A pdb=" N LEU A 173 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 493 Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 655 Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 707 Processing sheet with id=AA7, first strand: chain 'A' and resid 1022 through 1026 Processing sheet with id=AA8, first strand: chain 'A' and resid 1432 through 1434 removed outlier: 4.074A pdb=" N ASP A1432 " --> pdb=" O LEU A1580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1492 through 1493 removed outlier: 3.548A pdb=" N ILE A1471 " --> pdb=" O ILE A1492 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A1470 " --> pdb=" O VAL A1534 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A1533 " --> pdb=" O ILE A1543 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU A1545 " --> pdb=" O ALA A1533 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1658 through 1662 830 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4651 1.34 - 1.46: 3207 1.46 - 1.58: 6705 1.58 - 1.70: 1 1.70 - 1.82: 161 Bond restraints: 14725 Sorted by residual: bond pdb=" CB PRO A1585 " pdb=" CG PRO A1585 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.92e+00 bond pdb=" CG PRO A1585 " pdb=" CD PRO A1585 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.72e+00 bond pdb=" CB GLU D 150 " pdb=" CG GLU D 150 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CG1 ILE E 140 " pdb=" CD1 ILE E 140 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CB GLU A1234 " pdb=" CG GLU A1234 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 14720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 19792 2.62 - 5.25: 155 5.25 - 7.87: 27 7.87 - 10.49: 4 10.49 - 13.12: 4 Bond angle restraints: 19982 Sorted by residual: angle pdb=" CA PRO A1585 " pdb=" N PRO A1585 " pdb=" CD PRO A1585 " ideal model delta sigma weight residual 112.00 101.12 10.88 1.40e+00 5.10e-01 6.04e+01 angle pdb=" CA GLU D 150 " pdb=" CB GLU D 150 " pdb=" CG GLU D 150 " ideal model delta sigma weight residual 114.10 121.99 -7.89 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CB MET D 155 " pdb=" CG MET D 155 " pdb=" SD MET D 155 " ideal model delta sigma weight residual 112.70 124.43 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CA LEU A1457 " pdb=" CB LEU A1457 " pdb=" CG LEU A1457 " ideal model delta sigma weight residual 116.30 129.42 -13.12 3.50e+00 8.16e-02 1.40e+01 angle pdb=" C VAL A1611 " pdb=" N MET A1612 " pdb=" CA MET A1612 " ideal model delta sigma weight residual 121.14 114.58 6.56 1.75e+00 3.27e-01 1.40e+01 ... (remaining 19977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7757 17.97 - 35.95: 914 35.95 - 53.92: 210 53.92 - 71.90: 39 71.90 - 89.87: 11 Dihedral angle restraints: 8931 sinusoidal: 3560 harmonic: 5371 Sorted by residual: dihedral pdb=" CA ASP A 924 " pdb=" CB ASP A 924 " pdb=" CG ASP A 924 " pdb=" OD1 ASP A 924 " ideal model delta sinusoidal sigma weight residual -30.00 -89.68 59.68 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " pdb=" OD1 ASP A 358 " ideal model delta sinusoidal sigma weight residual -30.00 -86.74 56.74 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CG ARG A 464 " pdb=" CD ARG A 464 " pdb=" NE ARG A 464 " pdb=" CZ ARG A 464 " ideal model delta sinusoidal sigma weight residual 90.00 134.82 -44.82 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 8928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2088 0.067 - 0.133: 227 0.133 - 0.200: 2 0.200 - 0.266: 0 0.266 - 0.333: 1 Chirality restraints: 2318 Sorted by residual: chirality pdb=" CG LEU A1457 " pdb=" CB LEU A1457 " pdb=" CD1 LEU A1457 " pdb=" CD2 LEU A1457 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA PRO A1585 " pdb=" N PRO A1585 " pdb=" C PRO A1585 " pdb=" CB PRO A1585 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA MET A1612 " pdb=" N MET A1612 " pdb=" C MET A1612 " pdb=" CB MET A1612 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2315 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1584 " -0.062 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO A1585 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A1585 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1585 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1486 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO A1487 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A1487 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1487 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 901 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 902 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " 0.032 5.00e-02 4.00e+02 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 504 2.72 - 3.27: 14373 3.27 - 3.81: 24803 3.81 - 4.36: 27787 4.36 - 4.90: 48116 Nonbonded interactions: 115583 Sorted by model distance: nonbonded pdb=" OG SER A 141 " pdb=" OE1 GLU A 143 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP D 142 " pdb=" NZ LYS D 146 " model vdw 2.194 3.120 nonbonded pdb=" O ASP A 913 " pdb=" OG1 THR A 916 " model vdw 2.221 3.040 nonbonded pdb=" N GLU A 432 " pdb=" OE1 GLU A 432 " model vdw 2.261 3.120 nonbonded pdb=" N GLU A1234 " pdb=" OE1 GLU A1234 " model vdw 2.266 3.120 ... (remaining 115578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.020 Process input model: 13.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 0.149 14725 Z= 0.109 Angle : 0.581 13.117 19982 Z= 0.280 Chirality : 0.040 0.333 2318 Planarity : 0.004 0.086 2518 Dihedral : 16.128 89.870 5449 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.31 % Allowed : 23.47 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.21), residues: 1814 helix: 2.33 (0.17), residues: 980 sheet: 0.75 (0.58), residues: 86 loop : -0.39 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 880 TYR 0.013 0.001 TYR A1097 PHE 0.015 0.001 PHE A1343 TRP 0.031 0.001 TRP A 638 HIS 0.003 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (14725) covalent geometry : angle 0.58073 / 0.28 (19982) hydrogen bonds : bond 0.12167 / 8.42 ( 830) hydrogen bonds : angle 4.70150 / 3.43 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 316 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 TYR cc_start: 0.7667 (m-80) cc_final: 0.7232 (m-80) REVERT: A 1291 ASN cc_start: 0.8247 (t0) cc_final: 0.7831 (t0) REVERT: A 1341 PHE cc_start: 0.8975 (t80) cc_final: 0.8738 (t80) REVERT: A 1459 MET cc_start: 0.8257 (mmt) cc_final: 0.7713 (mmm) REVERT: A 1469 LEU cc_start: 0.9047 (tp) cc_final: 0.8810 (tm) REVERT: A 1489 LEU cc_start: 0.9091 (tp) cc_final: 0.8663 (tt) REVERT: A 1504 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7703 (mtp180) REVERT: A 1566 TYR cc_start: 0.8167 (m-80) cc_final: 0.7935 (m-10) REVERT: A 1616 MET cc_start: 0.7027 (ppp) cc_final: 0.5998 (pmm) REVERT: B 142 ASP cc_start: 0.8697 (t0) cc_final: 0.8358 (t0) REVERT: D 140 ILE cc_start: 0.9558 (pp) cc_final: 0.9186 (pp) REVERT: D 154 LEU cc_start: 0.9511 (tp) cc_final: 0.9291 (pp) outliers start: 5 outliers final: 0 residues processed: 318 average time/residue: 0.5067 time to fit residues: 179.1424 Evaluate side-chains 215 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1095 GLN ** A1408 ASN ** 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 = 0.4064 r_free = 0.4064 target = 0.142042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094607 restraints weight = 26054.841| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.10 r_work: 0.3096 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14725 Z= 0.153 Angle : 0.657 14.129 19982 Z= 0.314 Chirality : 0.042 0.261 2318 Planarity : 0.004 0.047 2518 Dihedral : 3.486 19.224 1994 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.81 % Allowed : 24.53 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.68 (0.20), residues: 1814 helix: 2.22 (0.17), residues: 983 sheet: 0.74 (0.55), residues: 97 loop : -0.36 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 132 TYR 0.016 0.001 TYR E 163 PHE 0.032 0.001 PHE A1426 TRP 0.022 0.001 TRP A 638 HIS 0.012 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (14725) covalent geometry : angle 0.65719 / 0.31 (19982) hydrogen bonds : bond 0.03777 / 2.61 ( 830) hydrogen bonds : angle 4.22409 / 3.15 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 223 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TRP cc_start: 0.8766 (t-100) cc_final: 0.8497 (t-100) REVERT: A 515 TYR cc_start: 0.8494 (m-80) cc_final: 0.7631 (m-80) REVERT: A 517 LYS cc_start: 0.8877 (tptt) cc_final: 0.8586 (tptt) REVERT: A 622 MET cc_start: 0.6779 (ttm) cc_final: 0.5684 (tpp) REVERT: A 706 GLU cc_start: 0.8262 (tp30) cc_final: 0.8056 (tp30) REVERT: A 1033 GLU cc_start: 0.8634 (pp20) cc_final: 0.8426 (pp20) REVERT: A 1291 ASN cc_start: 0.8701 (t0) cc_final: 0.8215 (t0) REVERT: A 1354 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8985 (pp) REVERT: A 1370 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7134 (m-70) REVERT: A 1374 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8018 (p0) REVERT: A 1459 MET cc_start: 0.8562 (mmt) cc_final: 0.7962 (mmm) REVERT: A 1469 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8603 (tm) REVERT: A 1566 TYR cc_start: 0.9123 (m-80) cc_final: 0.8803 (m-10) REVERT: A 1616 MET cc_start: 0.6943 (ppp) cc_final: 0.5896 (pmm) REVERT: B 142 ASP cc_start: 0.9004 (t0) cc_final: 0.8706 (t0) REVERT: C 149 MET cc_start: 0.6972 (mmt) cc_final: 0.6206 (mmp) REVERT: C 165 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.7232 (p) REVERT: D 143 ARG cc_start: 0.8955 (ptp-110) cc_final: 0.8744 (ptp-110) REVERT: D 145 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8579 (tmm) REVERT: D 151 THR cc_start: 0.8920 (t) cc_final: 0.8687 (p) REVERT: E 152 MET cc_start: 0.8198 (mmm) cc_final: 0.7850 (mmp) outliers start: 61 outliers final: 21 residues processed: 259 average time/residue: 0.4189 time to fit residues: 123.0854 Evaluate side-chains 223 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1469 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 163 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 84 optimal weight: 0.0670 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN A1050 HIS A1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.135780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.086238 restraints weight = 25854.407| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.05 r_work: 0.3068 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14725 Z= 0.191 Angle : 0.671 14.823 19982 Z= 0.318 Chirality : 0.043 0.227 2318 Planarity : 0.004 0.045 2518 Dihedral : 3.715 16.172 1994 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.56 % Allowed : 23.47 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.20), residues: 1814 helix: 2.13 (0.17), residues: 986 sheet: 0.61 (0.55), residues: 97 loop : -0.44 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 132 TYR 0.014 0.001 TYR A 853 PHE 0.019 0.001 PHE A1426 TRP 0.017 0.001 TRP A 638 HIS 0.010 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (14725) covalent geometry : angle 0.67088 / 0.32 (19982) hydrogen bonds : bond 0.04031 / 2.79 ( 830) hydrogen bonds : angle 4.25405 / 3.16 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 221 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8714 (p) REVERT: A 424 TRP cc_start: 0.8785 (t-100) cc_final: 0.8493 (t-100) REVERT: A 430 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8452 (tpp-160) REVERT: A 517 LYS cc_start: 0.9009 (tptt) cc_final: 0.8730 (tptp) REVERT: A 626 MET cc_start: 0.7125 (ppp) cc_final: 0.6524 (ptp) REVERT: A 1033 GLU cc_start: 0.8737 (pp20) cc_final: 0.8489 (pp20) REVERT: A 1039 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8110 (mt) REVERT: A 1183 PHE cc_start: 0.7883 (m-10) cc_final: 0.7637 (m-10) REVERT: A 1272 PHE cc_start: 0.9406 (m-80) cc_final: 0.8921 (m-10) REVERT: A 1291 ASN cc_start: 0.8743 (t0) cc_final: 0.8210 (t0) REVERT: A 1370 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7135 (m-70) REVERT: A 1374 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 1417 LYS cc_start: 0.9102 (mttm) cc_final: 0.8834 (mptp) REVERT: A 1459 MET cc_start: 0.8670 (mmt) cc_final: 0.8113 (mmm) REVERT: A 1469 LEU cc_start: 0.9004 (tp) cc_final: 0.8769 (tm) REVERT: A 1566 TYR cc_start: 0.9096 (m-80) cc_final: 0.8764 (m-10) REVERT: B 142 ASP cc_start: 0.9060 (t0) cc_final: 0.8772 (t0) REVERT: B 148 MET cc_start: 0.8209 (tpp) cc_final: 0.7938 (mmt) REVERT: B 152 MET cc_start: 0.8013 (tpp) cc_final: 0.7615 (tpt) REVERT: B 156 MET cc_start: 0.8272 (ptt) cc_final: 0.7903 (ptm) REVERT: D 143 ARG cc_start: 0.8990 (ptp-110) cc_final: 0.8701 (ptp-110) REVERT: D 156 MET cc_start: 0.9028 (mmm) cc_final: 0.8730 (tpp) outliers start: 73 outliers final: 24 residues processed: 265 average time/residue: 0.4314 time to fit residues: 128.4097 Evaluate side-chains 230 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1050 HIS Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 163 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 181 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1050 HIS A1095 GLN A1529 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086126 restraints weight = 25922.074| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.05 r_work: 0.3079 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14725 Z= 0.159 Angle : 0.675 15.211 19982 Z= 0.312 Chirality : 0.043 0.186 2318 Planarity : 0.004 0.050 2518 Dihedral : 3.751 16.201 1994 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.31 % Allowed : 23.28 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.20), residues: 1814 helix: 2.09 (0.17), residues: 985 sheet: 0.53 (0.55), residues: 97 loop : -0.47 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 815 TYR 0.011 0.001 TYR A1164 PHE 0.018 0.001 PHE A1426 TRP 0.018 0.001 TRP A 638 HIS 0.008 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (14725) covalent geometry : angle 0.67522 / 0.31 (19982) hydrogen bonds : bond 0.03751 / 2.59 ( 830) hydrogen bonds : angle 4.22530 / 3.16 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 211 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 424 TRP cc_start: 0.8804 (t-100) cc_final: 0.8509 (t-100) REVERT: A 430 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8491 (tpp-160) REVERT: A 511 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8044 (mp0) REVERT: A 517 LYS cc_start: 0.9052 (tptt) cc_final: 0.8730 (tptp) REVERT: A 626 MET cc_start: 0.7052 (ppp) cc_final: 0.6798 (ptp) REVERT: A 971 GLU cc_start: 0.8865 (tp30) cc_final: 0.8557 (mm-30) REVERT: A 1039 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 1183 PHE cc_start: 0.7895 (m-10) cc_final: 0.7633 (m-10) REVERT: A 1272 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8873 (m-10) REVERT: A 1291 ASN cc_start: 0.8732 (t0) cc_final: 0.8315 (t0) REVERT: A 1294 ARG cc_start: 0.8874 (ptp90) cc_final: 0.8620 (ptt-90) REVERT: A 1370 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7147 (m-70) REVERT: A 1374 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8027 (p0) REVERT: A 1417 LYS cc_start: 0.9103 (mttm) cc_final: 0.8822 (mptp) REVERT: A 1459 MET cc_start: 0.8716 (mmt) cc_final: 0.8131 (mmm) REVERT: A 1469 LEU cc_start: 0.9040 (tp) cc_final: 0.8811 (tm) REVERT: A 1566 TYR cc_start: 0.9093 (m-80) cc_final: 0.8753 (m-10) REVERT: A 1577 MET cc_start: 0.8552 (tpp) cc_final: 0.8282 (OUTLIER) REVERT: A 1616 MET cc_start: 0.6974 (ppp) cc_final: 0.6761 (ppp) REVERT: B 142 ASP cc_start: 0.9085 (t0) cc_final: 0.8802 (t0) REVERT: B 152 MET cc_start: 0.8034 (tpp) cc_final: 0.7687 (tpt) REVERT: B 156 MET cc_start: 0.8214 (ptt) cc_final: 0.7914 (ptm) REVERT: C 143 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8837 (mpp-170) REVERT: C 158 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7382 (ptpt) REVERT: D 143 ARG cc_start: 0.9031 (ptp-110) cc_final: 0.8706 (ptp-110) REVERT: D 156 MET cc_start: 0.9079 (mmm) cc_final: 0.8298 (tpt) outliers start: 69 outliers final: 26 residues processed: 254 average time/residue: 0.4361 time to fit residues: 123.8723 Evaluate side-chains 229 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1374 ASP Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1529 HIS Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain D residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 103 optimal weight: 0.0060 chunk 116 optimal weight: 0.9980 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 HIS A1050 HIS A1095 GLN ** A1485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.137124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087841 restraints weight = 25788.888| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.05 r_work: 0.3130 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14725 Z= 0.116 Angle : 0.656 14.804 19982 Z= 0.302 Chirality : 0.042 0.195 2318 Planarity : 0.003 0.042 2518 Dihedral : 3.691 17.119 1994 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.37 % Allowed : 24.03 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.20), residues: 1814 helix: 2.10 (0.17), residues: 979 sheet: 0.56 (0.55), residues: 96 loop : -0.40 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 132 TYR 0.012 0.001 TYR E 163 PHE 0.028 0.001 PHE A1343 TRP 0.026 0.001 TRP A 638 HIS 0.018 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14725) covalent geometry : angle 0.65575 / 0.30 (19982) hydrogen bonds : bond 0.03460 / 2.40 ( 830) hydrogen bonds : angle 4.16555 / 3.12 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.8440 (mp0) cc_final: 0.8084 (mp0) REVERT: A 171 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8636 (p) REVERT: A 424 TRP cc_start: 0.8804 (t-100) cc_final: 0.8546 (t-100) REVERT: A 488 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8110 (mtp85) REVERT: A 511 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8032 (mp0) REVERT: A 517 LYS cc_start: 0.9057 (tptt) cc_final: 0.8713 (tptp) REVERT: A 1039 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8140 (mt) REVERT: A 1068 VAL cc_start: 0.4836 (OUTLIER) cc_final: 0.4490 (p) REVERT: A 1183 PHE cc_start: 0.7816 (m-10) cc_final: 0.7550 (m-10) REVERT: A 1272 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.8851 (m-10) REVERT: A 1291 ASN cc_start: 0.8745 (t0) cc_final: 0.8314 (t0) REVERT: A 1309 ILE cc_start: 0.8786 (mm) cc_final: 0.8466 (pt) REVERT: A 1370 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.6990 (m-70) REVERT: A 1406 GLU cc_start: 0.8938 (pp20) cc_final: 0.8452 (pp20) REVERT: A 1417 LYS cc_start: 0.9073 (mttm) cc_final: 0.8765 (mptp) REVERT: A 1459 MET cc_start: 0.8720 (mmt) cc_final: 0.8109 (mmm) REVERT: A 1469 LEU cc_start: 0.9054 (tp) cc_final: 0.8840 (tm) REVERT: A 1530 ARG cc_start: 0.9302 (ttm-80) cc_final: 0.8968 (ttp80) REVERT: A 1566 TYR cc_start: 0.9095 (m-80) cc_final: 0.8760 (m-10) REVERT: A 1577 MET cc_start: 0.8686 (tpp) cc_final: 0.8448 (tpp) REVERT: A 1616 MET cc_start: 0.6847 (ppp) cc_final: 0.6566 (ppp) REVERT: B 142 ASP cc_start: 0.9104 (t0) cc_final: 0.8800 (t0) REVERT: B 152 MET cc_start: 0.8016 (tpp) cc_final: 0.7655 (tpt) REVERT: B 156 MET cc_start: 0.8182 (ptt) cc_final: 0.7971 (ptm) REVERT: C 143 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8853 (mpp-170) REVERT: D 143 ARG cc_start: 0.9014 (ptp-110) cc_final: 0.8716 (ptp-110) REVERT: D 156 MET cc_start: 0.9110 (mmm) cc_final: 0.8799 (tpp) outliers start: 54 outliers final: 19 residues processed: 245 average time/residue: 0.4972 time to fit residues: 136.0707 Evaluate side-chains 219 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 127 HIS Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 163 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 181 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN A 975 GLN A1050 HIS A1095 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087173 restraints weight = 25836.546| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.04 r_work: 0.3127 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14725 Z= 0.132 Angle : 0.671 14.640 19982 Z= 0.307 Chirality : 0.042 0.220 2318 Planarity : 0.003 0.034 2518 Dihedral : 3.669 17.305 1994 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.50 % Allowed : 24.28 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.20), residues: 1814 helix: 2.06 (0.17), residues: 987 sheet: 0.45 (0.55), residues: 97 loop : -0.44 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 132 TYR 0.011 0.001 TYR A1164 PHE 0.036 0.001 PHE A1343 TRP 0.024 0.001 TRP A 638 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14725) covalent geometry : angle 0.67053 / 0.31 (19982) hydrogen bonds : bond 0.03526 / 2.43 ( 830) hydrogen bonds : angle 4.16792 / 3.13 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.8457 (mp0) cc_final: 0.8092 (mp0) REVERT: A 424 TRP cc_start: 0.8883 (t-100) cc_final: 0.8579 (t-100) REVERT: A 488 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8111 (mtp85) REVERT: A 511 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8157 (mp0) REVERT: A 517 LYS cc_start: 0.9084 (tptt) cc_final: 0.8677 (tptp) REVERT: A 971 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8243 (mm-30) REVERT: A 975 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8417 (mp10) REVERT: A 1039 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 1068 VAL cc_start: 0.4867 (OUTLIER) cc_final: 0.4522 (p) REVERT: A 1085 ASN cc_start: 0.8355 (m110) cc_final: 0.8104 (p0) REVERT: A 1183 PHE cc_start: 0.7835 (m-10) cc_final: 0.7575 (m-10) REVERT: A 1272 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8858 (m-10) REVERT: A 1291 ASN cc_start: 0.8891 (t0) cc_final: 0.8422 (t0) REVERT: A 1309 ILE cc_start: 0.8812 (mm) cc_final: 0.8495 (pt) REVERT: A 1370 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.6965 (m-70) REVERT: A 1406 GLU cc_start: 0.9059 (pp20) cc_final: 0.8736 (pp20) REVERT: A 1417 LYS cc_start: 0.9022 (mttm) cc_final: 0.8747 (mptp) REVERT: A 1459 MET cc_start: 0.8703 (mmt) cc_final: 0.8075 (mmm) REVERT: A 1469 LEU cc_start: 0.9078 (tp) cc_final: 0.8869 (tm) REVERT: A 1530 ARG cc_start: 0.9341 (ttm-80) cc_final: 0.8996 (ttp80) REVERT: A 1566 TYR cc_start: 0.9094 (m-80) cc_final: 0.8738 (m-10) REVERT: A 1577 MET cc_start: 0.8729 (tpp) cc_final: 0.8501 (tpp) REVERT: A 1616 MET cc_start: 0.6893 (ppp) cc_final: 0.6643 (ppp) REVERT: B 142 ASP cc_start: 0.9113 (t0) cc_final: 0.8822 (t0) REVERT: B 148 MET cc_start: 0.8617 (mmm) cc_final: 0.8406 (mtt) REVERT: D 143 ARG cc_start: 0.9033 (ptp-110) cc_final: 0.8718 (ptp-110) outliers start: 56 outliers final: 26 residues processed: 247 average time/residue: 0.4784 time to fit residues: 132.2574 Evaluate side-chains 230 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1508 MET Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 163 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 129 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1025 HIS A1050 HIS A1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081833 restraints weight = 25634.165| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.00 r_work: 0.3007 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14725 Z= 0.242 Angle : 0.748 15.451 19982 Z= 0.348 Chirality : 0.046 0.234 2318 Planarity : 0.004 0.046 2518 Dihedral : 3.964 17.836 1994 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.53 % Rotamer: Outliers : 4.06 % Allowed : 24.53 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.20), residues: 1814 helix: 1.85 (0.17), residues: 993 sheet: 0.17 (0.55), residues: 99 loop : -0.47 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 132 TYR 0.016 0.001 TYR A1164 PHE 0.024 0.002 PHE A1343 TRP 0.019 0.002 TRP A 638 HIS 0.007 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (14725) covalent geometry : angle 0.74798 / 0.35 (19982) hydrogen bonds : bond 0.04121 / 2.82 ( 830) hydrogen bonds : angle 4.34781 / 3.25 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.8345 (mp0) cc_final: 0.8064 (mp0) REVERT: A 171 SER cc_start: 0.9224 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 424 TRP cc_start: 0.8893 (t-100) cc_final: 0.8588 (t-100) REVERT: A 511 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8119 (mp0) REVERT: A 517 LYS cc_start: 0.9233 (tptt) cc_final: 0.8839 (tptp) REVERT: A 647 ASN cc_start: 0.8937 (t0) cc_final: 0.8696 (t0) REVERT: A 971 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8315 (mm-30) REVERT: A 1039 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8293 (mt) REVERT: A 1272 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: A 1291 ASN cc_start: 0.8850 (t0) cc_final: 0.8430 (t0) REVERT: A 1309 ILE cc_start: 0.8856 (mm) cc_final: 0.8541 (pt) REVERT: A 1370 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7095 (m-70) REVERT: A 1406 GLU cc_start: 0.9122 (pp20) cc_final: 0.8873 (pp20) REVERT: A 1417 LYS cc_start: 0.9019 (mttm) cc_final: 0.8707 (mptp) REVERT: A 1459 MET cc_start: 0.8772 (mmt) cc_final: 0.8188 (mmm) REVERT: A 1469 LEU cc_start: 0.9125 (tp) cc_final: 0.8900 (tm) REVERT: A 1577 MET cc_start: 0.8822 (tpp) cc_final: 0.8593 (tpp) REVERT: A 1616 MET cc_start: 0.7056 (ppp) cc_final: 0.6851 (ppp) REVERT: B 133 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8614 (pp) REVERT: B 142 ASP cc_start: 0.9155 (t0) cc_final: 0.8864 (t70) REVERT: B 152 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7972 (tmm) REVERT: C 158 LYS cc_start: 0.8339 (ttpp) cc_final: 0.8051 (ttmt) REVERT: D 145 MET cc_start: 0.8797 (ttt) cc_final: 0.8596 (tmm) REVERT: D 155 MET cc_start: 0.9323 (tpp) cc_final: 0.9045 (tpp) REVERT: D 160 ASP cc_start: 0.9466 (m-30) cc_final: 0.9226 (m-30) outliers start: 65 outliers final: 27 residues processed: 248 average time/residue: 0.4381 time to fit residues: 121.8204 Evaluate side-chains 234 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1508 MET Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain E residue 163 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 177 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 157 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 GLN A1050 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.134353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084957 restraints weight = 25665.844| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.99 r_work: 0.3079 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14725 Z= 0.139 Angle : 0.742 15.541 19982 Z= 0.338 Chirality : 0.043 0.217 2318 Planarity : 0.003 0.042 2518 Dihedral : 3.871 17.240 1994 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 2.75 % Allowed : 26.40 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.20), residues: 1814 helix: 1.87 (0.16), residues: 994 sheet: 0.26 (0.55), residues: 97 loop : -0.52 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 815 TYR 0.010 0.001 TYR A1164 PHE 0.033 0.001 PHE A1343 TRP 0.025 0.001 TRP A 638 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (14725) covalent geometry : angle 0.74195 / 0.34 (19982) hydrogen bonds : bond 0.03655 / 2.52 ( 830) hydrogen bonds : angle 4.30316 / 3.23 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.8356 (mp0) cc_final: 0.7984 (mp0) REVERT: A 424 TRP cc_start: 0.8917 (t-100) cc_final: 0.8609 (t-100) REVERT: A 511 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8279 (mp0) REVERT: A 517 LYS cc_start: 0.9204 (tptt) cc_final: 0.8800 (tptp) REVERT: A 647 ASN cc_start: 0.8940 (t0) cc_final: 0.8667 (t0) REVERT: A 971 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 975 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8197 (mm110) REVERT: A 1068 VAL cc_start: 0.4950 (OUTLIER) cc_final: 0.4622 (p) REVERT: A 1272 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: A 1291 ASN cc_start: 0.8723 (t0) cc_final: 0.8268 (t0) REVERT: A 1309 ILE cc_start: 0.8851 (mm) cc_final: 0.8530 (pt) REVERT: A 1370 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7050 (m-70) REVERT: A 1406 GLU cc_start: 0.9189 (pp20) cc_final: 0.8332 (tm-30) REVERT: A 1417 LYS cc_start: 0.9010 (mttm) cc_final: 0.8694 (mptp) REVERT: A 1459 MET cc_start: 0.8744 (mmt) cc_final: 0.8103 (mmm) REVERT: A 1469 LEU cc_start: 0.9139 (tp) cc_final: 0.8916 (tm) REVERT: A 1566 TYR cc_start: 0.9100 (m-80) cc_final: 0.8802 (m-10) REVERT: A 1577 MET cc_start: 0.8750 (tpp) cc_final: 0.8513 (tpp) REVERT: A 1616 MET cc_start: 0.7057 (ppp) cc_final: 0.6851 (ppp) REVERT: B 142 ASP cc_start: 0.9145 (t0) cc_final: 0.8925 (t70) REVERT: B 152 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7978 (tmm) REVERT: C 143 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8872 (mpp-170) REVERT: C 148 MET cc_start: 0.7838 (mmm) cc_final: 0.7466 (mmm) REVERT: D 145 MET cc_start: 0.8833 (ttt) cc_final: 0.8522 (tmm) REVERT: D 155 MET cc_start: 0.9306 (tpp) cc_final: 0.9071 (tpp) REVERT: D 156 MET cc_start: 0.9122 (tpp) cc_final: 0.8870 (mmm) REVERT: E 142 ASP cc_start: 0.9251 (t0) cc_final: 0.8791 (t0) REVERT: E 146 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8539 (mmtt) REVERT: E 157 GLU cc_start: 0.8222 (pt0) cc_final: 0.7908 (pm20) outliers start: 44 outliers final: 17 residues processed: 233 average time/residue: 0.4553 time to fit residues: 118.2826 Evaluate side-chains 223 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 161 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 160 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 169 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 136 optimal weight: 0.0470 chunk 64 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 900 GLN A1050 HIS A1095 GLN ** A1485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086010 restraints weight = 25898.391| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.03 r_work: 0.3093 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14725 Z= 0.126 Angle : 0.749 15.565 19982 Z= 0.341 Chirality : 0.042 0.238 2318 Planarity : 0.003 0.062 2518 Dihedral : 3.786 17.057 1994 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 1.94 % Allowed : 26.90 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.20), residues: 1814 helix: 1.87 (0.17), residues: 994 sheet: 0.27 (0.55), residues: 97 loop : -0.48 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 58 TYR 0.013 0.001 TYR A1443 PHE 0.017 0.001 PHE A 230 TRP 0.033 0.001 TRP A 638 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14725) covalent geometry : angle 0.74895 / 0.34 (19982) hydrogen bonds : bond 0.03516 / 2.43 ( 830) hydrogen bonds : angle 4.29962 / 3.25 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 143 GLU cc_start: 0.8375 (mp0) cc_final: 0.7994 (mp0) REVERT: A 424 TRP cc_start: 0.8913 (t-100) cc_final: 0.8599 (t-100) REVERT: A 488 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8178 (mtp85) REVERT: A 511 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8278 (mp0) REVERT: A 517 LYS cc_start: 0.9198 (tptt) cc_final: 0.8820 (tptp) REVERT: A 647 ASN cc_start: 0.8940 (t0) cc_final: 0.8650 (t0) REVERT: A 971 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8159 (mm-30) REVERT: A 975 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8181 (mm110) REVERT: A 1068 VAL cc_start: 0.4890 (OUTLIER) cc_final: 0.4567 (p) REVERT: A 1272 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8827 (m-10) REVERT: A 1291 ASN cc_start: 0.8596 (t0) cc_final: 0.8160 (t0) REVERT: A 1309 ILE cc_start: 0.8852 (mm) cc_final: 0.8538 (pt) REVERT: A 1370 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.6979 (m-70) REVERT: A 1406 GLU cc_start: 0.9235 (pp20) cc_final: 0.8554 (tm-30) REVERT: A 1455 GLN cc_start: 0.8777 (mm110) cc_final: 0.8506 (mp10) REVERT: A 1459 MET cc_start: 0.8728 (mmt) cc_final: 0.8123 (mmm) REVERT: A 1469 LEU cc_start: 0.9132 (tp) cc_final: 0.8928 (tm) REVERT: A 1566 TYR cc_start: 0.9120 (m-80) cc_final: 0.8805 (m-10) REVERT: A 1577 MET cc_start: 0.8751 (tpp) cc_final: 0.8514 (tpp) REVERT: A 1616 MET cc_start: 0.7061 (ppp) cc_final: 0.6832 (ppp) REVERT: B 142 ASP cc_start: 0.9124 (t0) cc_final: 0.8844 (t0) REVERT: B 152 MET cc_start: 0.8232 (mmm) cc_final: 0.8015 (tpt) REVERT: C 143 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8858 (mpp-170) REVERT: C 148 MET cc_start: 0.7866 (mmm) cc_final: 0.7549 (OUTLIER) REVERT: C 158 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7689 (ptpp) REVERT: D 143 ARG cc_start: 0.9086 (ptp-110) cc_final: 0.8728 (ptp-110) REVERT: D 145 MET cc_start: 0.8819 (ttt) cc_final: 0.8476 (tmm) REVERT: D 156 MET cc_start: 0.9175 (tpp) cc_final: 0.8807 (mmm) REVERT: E 139 LYS cc_start: 0.8964 (mmpt) cc_final: 0.8451 (mmmt) REVERT: E 157 GLU cc_start: 0.8167 (pt0) cc_final: 0.7841 (pm20) outliers start: 31 outliers final: 20 residues processed: 235 average time/residue: 0.4563 time to fit residues: 119.3820 Evaluate side-chains 219 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1370 HIS Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 843 ASN A1050 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083613 restraints weight = 25783.158| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.98 r_work: 0.3034 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14725 Z= 0.185 Angle : 0.780 15.835 19982 Z= 0.359 Chirality : 0.045 0.369 2318 Planarity : 0.004 0.032 2518 Dihedral : 3.881 17.860 1994 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 27.72 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.20), residues: 1814 helix: 1.82 (0.17), residues: 995 sheet: 0.23 (0.55), residues: 97 loop : -0.50 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 815 TYR 0.025 0.001 TYR E 163 PHE 0.018 0.001 PHE A 230 TRP 0.024 0.001 TRP A 638 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (14725) covalent geometry : angle 0.78026 / 0.36 (19982) hydrogen bonds : bond 0.03881 / 2.66 ( 830) hydrogen bonds : angle 4.40194 / 3.33 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TRP cc_start: 0.8943 (t-100) cc_final: 0.8644 (t-100) REVERT: A 511 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8358 (mp0) REVERT: A 517 LYS cc_start: 0.9281 (tptt) cc_final: 0.8898 (tptp) REVERT: A 647 ASN cc_start: 0.8979 (t0) cc_final: 0.8719 (t0) REVERT: A 971 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 975 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8226 (mm110) REVERT: A 1068 VAL cc_start: 0.5023 (OUTLIER) cc_final: 0.4722 (p) REVERT: A 1272 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8852 (m-80) REVERT: A 1291 ASN cc_start: 0.8563 (t0) cc_final: 0.8131 (t0) REVERT: A 1309 ILE cc_start: 0.8870 (mm) cc_final: 0.8548 (pt) REVERT: A 1406 GLU cc_start: 0.9293 (pp20) cc_final: 0.8672 (tm-30) REVERT: A 1459 MET cc_start: 0.8758 (mmt) cc_final: 0.8169 (mmm) REVERT: A 1469 LEU cc_start: 0.9151 (tp) cc_final: 0.8924 (tm) REVERT: A 1566 TYR cc_start: 0.9132 (m-80) cc_final: 0.8801 (m-10) REVERT: A 1577 MET cc_start: 0.8765 (tpp) cc_final: 0.8513 (tpp) REVERT: A 1616 MET cc_start: 0.7053 (ppp) cc_final: 0.6829 (ppp) REVERT: B 142 ASP cc_start: 0.9145 (t0) cc_final: 0.8841 (t0) REVERT: C 148 MET cc_start: 0.8008 (mmm) cc_final: 0.7605 (OUTLIER) REVERT: C 158 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8089 (ttmt) REVERT: D 143 ARG cc_start: 0.9107 (ptp-110) cc_final: 0.8768 (ptp-110) REVERT: D 145 MET cc_start: 0.8791 (ttt) cc_final: 0.8408 (tmm) REVERT: D 150 GLU cc_start: 0.9266 (pp20) cc_final: 0.9046 (pp20) REVERT: D 156 MET cc_start: 0.9061 (tpp) cc_final: 0.8813 (mmm) REVERT: E 146 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8713 (mmtt) outliers start: 31 outliers final: 25 residues processed: 228 average time/residue: 0.4424 time to fit residues: 112.8970 Evaluate side-chains 223 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1272 PHE Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain E residue 163 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1050 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084734 restraints weight = 25820.639| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.99 r_work: 0.3068 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14725 Z= 0.146 Angle : 0.791 17.054 19982 Z= 0.362 Chirality : 0.044 0.375 2318 Planarity : 0.004 0.056 2518 Dihedral : 3.854 17.631 1994 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.31 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 27.65 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.20), residues: 1814 helix: 1.82 (0.17), residues: 996 sheet: 0.26 (0.55), residues: 97 loop : -0.49 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 58 TYR 0.023 0.001 TYR E 163 PHE 0.017 0.001 PHE A 230 TRP 0.028 0.001 TRP A 638 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14725) covalent geometry : angle 0.79107 / 0.36 (19982) hydrogen bonds : bond 0.03740 / 2.57 ( 830) hydrogen bonds : angle 4.38598 / 3.32 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5362.98 seconds wall clock time: 92 minutes 9.76 seconds (5529.76 seconds total)