Starting phenix.real_space_refine on Wed Mar 4 06:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ckl_30387/03_2026/7ckl_30387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckl_30387/03_2026/7ckl_30387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ckl_30387/03_2026/7ckl_30387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckl_30387/03_2026/7ckl_30387.map" model { file = "/net/cci-nas-00/data/ceres_data/7ckl_30387/03_2026/7ckl_30387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckl_30387/03_2026/7ckl_30387.cif" } resolution = 3.88 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= 0.007 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 S 82 5.16 5 C 7343 2.51 5 N 1938 2.21 5 O 2155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11521 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1415, 11137 Classifications: {'peptide': 1415} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 43, 'TRANS': 1371} Chain breaks: 17 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 9, 'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11192 SG CYS B 31 16.943 55.949 31.813 1.00125.91 S ATOM 11213 SG CYS B 34 17.543 60.081 32.522 1.00113.55 S ATOM 11350 SG CYS B 50 15.013 58.009 29.830 1.00158.06 S ATOM 11372 SG CYS B 53 18.328 57.675 29.156 1.00152.26 S ATOM 11298 SG CYS B 44 17.566 45.961 30.824 1.00171.86 S ATOM 11451 SG CYS B 64 20.438 47.396 29.537 1.00165.66 S ATOM 11472 SG CYS B 67 20.599 45.550 32.419 1.00176.90 S Time building chain proxies: 2.55, per 1000 atoms: 0.22 Number of scatterers: 11521 At special positions: 0 Unit cell: (123.76, 114.24, 116.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 82 16.00 O 2155 8.00 N 1938 7.00 C 7343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1692 " - pdb=" SG CYS A1792 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 538.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 50 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 34 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 44 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 64 " Number of angles added : 9 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 58.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 4.021A pdb=" N ILE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 3.624A pdb=" N GLN A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 108 through 132 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.613A pdb=" N LYS A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 340 through 363 removed outlier: 3.790A pdb=" N ARG A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.054A pdb=" N VAL A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.590A pdb=" N ARG A 581 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 582 " --> pdb=" O PRO A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 589 through 603 removed outlier: 4.401A pdb=" N GLN A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 4.645A pdb=" N ASN A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 650 removed outlier: 4.048A pdb=" N VAL A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.723A pdb=" N LEU A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 707 removed outlier: 3.603A pdb=" N ARG A 697 " --> pdb=" O MET A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 717 through 737 removed outlier: 3.683A pdb=" N ASP A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.662A pdb=" N LEU A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 873 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 902 through 910 removed outlier: 3.556A pdb=" N SER A 910 " --> pdb=" O ASP A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 1139 through 1159 Processing helix chain 'A' and resid 1167 through 1184 removed outlier: 3.629A pdb=" N MET A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.662A pdb=" N MET A1200 " --> pdb=" O TRP A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1211 removed outlier: 3.619A pdb=" N PHE A1205 " --> pdb=" O CYS A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1238 Processing helix chain 'A' and resid 1244 through 1261 removed outlier: 3.531A pdb=" N VAL A1248 " --> pdb=" O PRO A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1280 Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.523A pdb=" N PHE A1354 " --> pdb=" O ASP A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1409 removed outlier: 3.590A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1433 Processing helix chain 'A' and resid 1435 through 1453 removed outlier: 3.766A pdb=" N CYS A1439 " --> pdb=" O PRO A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1490 through 1508 removed outlier: 3.750A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A1508 " --> pdb=" O ASN A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1520 removed outlier: 3.560A pdb=" N THR A1516 " --> pdb=" O HIS A1512 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1536 removed outlier: 3.968A pdb=" N LYS A1529 " --> pdb=" O LEU A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1586 removed outlier: 4.177A pdb=" N ILE A1586 " --> pdb=" O ILE A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 Processing helix chain 'A' and resid 1640 through 1650 removed outlier: 3.528A pdb=" N ILE A1644 " --> pdb=" O TYR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1681 Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1744 through 1753 Processing helix chain 'A' and resid 1753 through 1759 Processing helix chain 'A' and resid 1782 through 1791 removed outlier: 4.741A pdb=" N ASP A1789 " --> pdb=" O CYS A1785 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A1790 " --> pdb=" O VAL A1786 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A1791 " --> pdb=" O ALA A1787 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.690A pdb=" N GLY A 90 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 100 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 6.096A pdb=" N LEU A 207 " --> pdb=" O TYR A1109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.837A pdb=" N ARG A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 537 through 542 removed outlier: 6.598A pdb=" N LYS A 560 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR A 576 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 562 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 574 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 564 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1133 through 1138 removed outlier: 7.231A pdb=" N PHE A1121 " --> pdb=" O GLU A1242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1326 through 1330 Processing sheet with id=AA8, first strand: chain 'A' and resid 1383 through 1385 Processing sheet with id=AA9, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AB1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.604A pdb=" N VAL A1631 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 43 613 hydrogen bonds defined for protein. 1785 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: 1.99 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3724 1.35 - 1.46: 2639 1.46 - 1.58: 5241 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 11725 Sorted by residual: bond pdb=" N ASP A1467 " pdb=" CA ASP A1467 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.22e-02 6.72e+03 6.71e+00 bond pdb=" C PHE A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 1.337 1.351 -0.014 9.80e-03 1.04e+04 2.06e+00 bond pdb=" CA VAL A1434 " pdb=" CB VAL A1434 " ideal model delta sigma weight residual 1.537 1.524 0.014 1.29e-02 6.01e+03 1.12e+00 bond pdb=" C VAL A1468 " pdb=" O VAL A1468 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.19e-02 7.06e+03 1.06e+00 bond pdb=" C TRP A1392 " pdb=" O TRP A1392 " ideal model delta sigma weight residual 1.235 1.247 -0.011 1.12e-02 7.97e+03 1.03e+00 ... (remaining 11720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 15538 1.67 - 3.34: 241 3.34 - 5.01: 43 5.01 - 6.68: 6 6.68 - 8.34: 4 Bond angle restraints: 15832 Sorted by residual: angle pdb=" N ARG A1469 " pdb=" CA ARG A1469 " pdb=" C ARG A1469 " ideal model delta sigma weight residual 114.62 107.07 7.55 1.14e+00 7.69e-01 4.39e+01 angle pdb=" C ASP A1467 " pdb=" N VAL A1468 " pdb=" CA VAL A1468 " ideal model delta sigma weight residual 121.97 130.31 -8.34 1.80e+00 3.09e-01 2.15e+01 angle pdb=" CA GLU A 929 " pdb=" C GLU A 929 " pdb=" N PRO A 930 " ideal model delta sigma weight residual 120.81 117.23 3.58 8.60e-01 1.35e+00 1.73e+01 angle pdb=" N ASP A1467 " pdb=" CA ASP A1467 " pdb=" C ASP A1467 " ideal model delta sigma weight residual 111.56 106.02 5.54 1.38e+00 5.25e-01 1.61e+01 angle pdb=" O ASP A1467 " pdb=" C ASP A1467 " pdb=" N VAL A1468 " ideal model delta sigma weight residual 122.19 127.11 -4.92 1.34e+00 5.57e-01 1.35e+01 ... (remaining 15827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6530 17.74 - 35.47: 498 35.47 - 53.21: 73 53.21 - 70.95: 9 70.95 - 88.68: 15 Dihedral angle restraints: 7125 sinusoidal: 2824 harmonic: 4301 Sorted by residual: dihedral pdb=" CA VAL A1468 " pdb=" C VAL A1468 " pdb=" N ARG A1469 " pdb=" CA ARG A1469 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR A 746 " pdb=" C THR A 746 " pdb=" N ALA A 747 " pdb=" CA ALA A 747 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " pdb=" CD GLU A 41 " pdb=" OE1 GLU A 41 " ideal model delta sinusoidal sigma weight residual 0.00 -88.35 88.35 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1295 0.037 - 0.074: 407 0.074 - 0.111: 101 0.111 - 0.148: 14 0.148 - 0.185: 2 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CB ILE A 451 " pdb=" CA ILE A 451 " pdb=" CG1 ILE A 451 " pdb=" CG2 ILE A 451 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA ILE A 667 " pdb=" N ILE A 667 " pdb=" C ILE A 667 " pdb=" CB ILE A 667 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1816 not shown) Planarity restraints: 2001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1396 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A1397 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1397 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1397 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1414 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A1415 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1415 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1415 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1468 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C VAL A1468 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A1468 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A1469 " 0.008 2.00e-02 2.50e+03 ... (remaining 1998 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2450 2.78 - 3.31: 11760 3.31 - 3.84: 18557 3.84 - 4.37: 21087 4.37 - 4.90: 35793 Nonbonded interactions: 89647 Sorted by model distance: nonbonded pdb=" O ASP A 129 " pdb=" OG SER A 132 " model vdw 2.244 3.040 nonbonded pdb=" O GLU A1523 " pdb=" OG SER A1527 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR A1519 " pdb=" O SER A1527 " model vdw 2.263 3.040 nonbonded pdb=" O GLN A 172 " pdb=" OG SER A 176 " model vdw 2.267 3.040 nonbonded pdb=" O ILE A1648 " pdb=" OG1 THR A1651 " model vdw 2.269 3.040 ... (remaining 89642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 11734 Z= 0.143 Angle : 0.698 20.607 15843 Z= 0.333 Chirality : 0.038 0.185 1819 Planarity : 0.003 0.040 2001 Dihedral : 13.089 88.684 4318 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % 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: -2.17 (0.20), residues: 1426 helix: -0.18 (0.16), residues: 792 sheet: -1.51 (0.52), residues: 92 loop : -3.41 (0.21), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1476 TYR 0.008 0.001 TYR A 654 PHE 0.015 0.001 PHE A 541 TRP 0.007 0.001 TRP A1666 HIS 0.003 0.001 HIS A1287 Details of bonding type rmsd covalent geometry : bond 0.00243 (11725) covalent geometry : angle 0.56022 (15832) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.92409 ( 2) hydrogen bonds : bond 0.12117 ( 613) hydrogen bonds : angle 4.79178 ( 1785) metal coordination : bond 0.10042 ( 8) metal coordination : angle 17.48171 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 LEU cc_start: 0.8757 (mt) cc_final: 0.8530 (mt) REVERT: A 456 TYR cc_start: 0.7543 (t80) cc_final: 0.6928 (t80) REVERT: A 511 LYS cc_start: 0.8365 (pptt) cc_final: 0.8144 (pttm) REVERT: A 593 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7889 (tp-100) REVERT: A 647 MET cc_start: 0.8154 (tpt) cc_final: 0.7927 (tpt) REVERT: A 664 GLU cc_start: 0.7943 (tp30) cc_final: 0.7475 (tp30) REVERT: A 665 GLU cc_start: 0.8031 (tt0) cc_final: 0.7813 (mm-30) REVERT: A 753 ASP cc_start: 0.8306 (m-30) cc_final: 0.7544 (m-30) REVERT: A 1150 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7289 (tp30) REVERT: A 1154 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8158 (tp30) REVERT: A 1199 MET cc_start: 0.8216 (mmt) cc_final: 0.7895 (mmt) REVERT: A 1240 MET cc_start: 0.6876 (mtt) cc_final: 0.6591 (mtt) REVERT: A 1299 LEU cc_start: 0.8694 (mt) cc_final: 0.8488 (mt) REVERT: A 1300 HIS cc_start: 0.7523 (t-170) cc_final: 0.7077 (t-170) REVERT: A 1301 ASN cc_start: 0.8892 (m-40) cc_final: 0.8018 (m-40) REVERT: A 1408 HIS cc_start: 0.6761 (m-70) cc_final: 0.6558 (m90) REVERT: A 1463 ASN cc_start: 0.8436 (t0) cc_final: 0.8216 (t0) REVERT: A 1470 ASP cc_start: 0.7427 (p0) cc_final: 0.7123 (p0) REVERT: A 1531 LEU cc_start: 0.8981 (pp) cc_final: 0.8745 (pp) REVERT: A 1672 LEU cc_start: 0.8063 (tp) cc_final: 0.7863 (tt) REVERT: B 26 LEU cc_start: 0.6300 (mp) cc_final: 0.5623 (mp) REVERT: B 43 GLU cc_start: 0.8983 (tt0) cc_final: 0.8641 (tp30) REVERT: B 47 HIS cc_start: 0.7851 (p90) cc_final: 0.7501 (p90) REVERT: B 48 TYR cc_start: 0.8301 (m-10) cc_final: 0.8021 (m-10) REVERT: B 51 LEU cc_start: 0.8946 (tp) cc_final: 0.8731 (tt) REVERT: B 56 LEU cc_start: 0.8743 (tp) cc_final: 0.8434 (tt) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1009 time to fit residues: 46.9351 Evaluate side-chains 227 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 290 GLN A 321 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN A 593 GLN A 655 HIS A 703 ASN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 ASN A1287 HIS A1315 ASN A1408 HIS A1432 ASN A1483 GLN A1504 ASN A1518 ASN A1587 GLN A1638 ASN A1664 GLN B 52 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.155232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.110933 restraints weight = 22082.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111578 restraints weight = 12669.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.112555 restraints weight = 9709.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113771 restraints weight = 7744.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113904 restraints weight = 6534.406| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11734 Z= 0.113 Angle : 0.622 10.044 15843 Z= 0.304 Chirality : 0.040 0.181 1819 Planarity : 0.004 0.043 2001 Dihedral : 3.900 23.588 1557 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.34 % Rotamer: Outliers : 1.41 % Allowed : 12.33 % Favored : 86.25 % 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: -0.99 (0.22), residues: 1426 helix: 0.88 (0.18), residues: 801 sheet: -1.26 (0.53), residues: 89 loop : -3.05 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1501 TYR 0.014 0.001 TYR A1228 PHE 0.028 0.001 PHE A1274 TRP 0.020 0.001 TRP A1688 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00241 (11725) covalent geometry : angle 0.61753 (15832) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.70950 ( 2) hydrogen bonds : bond 0.03473 ( 613) hydrogen bonds : angle 3.95830 ( 1785) metal coordination : bond 0.00425 ( 8) metal coordination : angle 3.09026 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 LEU cc_start: 0.8508 (mt) cc_final: 0.8159 (mt) REVERT: A 333 LYS cc_start: 0.8221 (tptt) cc_final: 0.7896 (tppt) REVERT: A 456 TYR cc_start: 0.7896 (t80) cc_final: 0.7482 (t80) REVERT: A 510 MET cc_start: 0.8240 (ttt) cc_final: 0.8020 (tpt) REVERT: A 511 LYS cc_start: 0.8477 (pptt) cc_final: 0.8199 (pttm) REVERT: A 593 GLN cc_start: 0.8453 (tp40) cc_final: 0.7930 (tp-100) REVERT: A 621 LYS cc_start: 0.8877 (tttt) cc_final: 0.8647 (mtpt) REVERT: A 647 MET cc_start: 0.8202 (tpt) cc_final: 0.7998 (tpt) REVERT: A 755 MET cc_start: 0.9015 (tpp) cc_final: 0.8796 (tpt) REVERT: A 786 LEU cc_start: 0.9273 (tp) cc_final: 0.9035 (tp) REVERT: A 1094 MET cc_start: 0.6833 (tpt) cc_final: 0.6583 (tpt) REVERT: A 1134 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7652 (mm-30) REVERT: A 1144 MET cc_start: 0.8207 (ttm) cc_final: 0.7899 (mtt) REVERT: A 1147 ARG cc_start: 0.8110 (tpt90) cc_final: 0.7906 (ptm-80) REVERT: A 1150 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7875 (tp30) REVERT: A 1154 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8109 (tp30) REVERT: A 1191 MET cc_start: 0.7733 (mtp) cc_final: 0.7082 (mpp) REVERT: A 1199 MET cc_start: 0.8482 (mmt) cc_final: 0.8108 (mmt) REVERT: A 1240 MET cc_start: 0.6504 (mtt) cc_final: 0.6287 (mtt) REVERT: A 1276 TYR cc_start: 0.8150 (m-80) cc_final: 0.7860 (m-80) REVERT: A 1299 LEU cc_start: 0.8906 (mt) cc_final: 0.8539 (mt) REVERT: A 1300 HIS cc_start: 0.7684 (t-170) cc_final: 0.7290 (t-170) REVERT: A 1301 ASN cc_start: 0.8868 (m-40) cc_final: 0.7968 (m-40) REVERT: A 1312 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7816 (mtp85) REVERT: A 1524 HIS cc_start: 0.8935 (m90) cc_final: 0.8532 (m-70) REVERT: A 1793 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7625 (mp0) REVERT: B 43 GLU cc_start: 0.9031 (tt0) cc_final: 0.8696 (tp30) REVERT: B 48 TYR cc_start: 0.8463 (m-10) cc_final: 0.8087 (m-10) outliers start: 18 outliers final: 9 residues processed: 267 average time/residue: 0.0932 time to fit residues: 36.4824 Evaluate side-chains 233 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 7 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 0.0570 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 GLN A1335 GLN ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.150380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104931 restraints weight = 22793.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.105450 restraints weight = 13751.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107231 restraints weight = 9953.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107546 restraints weight = 7847.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107766 restraints weight = 7179.898| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11734 Z= 0.155 Angle : 0.645 9.986 15843 Z= 0.317 Chirality : 0.041 0.200 1819 Planarity : 0.004 0.049 2001 Dihedral : 4.086 20.917 1557 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 1.81 % Allowed : 15.79 % Favored : 82.40 % 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: -0.53 (0.22), residues: 1426 helix: 1.25 (0.18), residues: 804 sheet: -0.85 (0.57), residues: 79 loop : -2.89 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1226 TYR 0.014 0.001 TYR A 562 PHE 0.034 0.002 PHE A1214 TRP 0.009 0.001 TRP A 325 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00346 (11725) covalent geometry : angle 0.63827 (15832) SS BOND : bond 0.00385 ( 1) SS BOND : angle 0.82163 ( 2) hydrogen bonds : bond 0.03598 ( 613) hydrogen bonds : angle 3.97652 ( 1785) metal coordination : bond 0.00634 ( 8) metal coordination : angle 3.91250 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6701 (mmt-90) REVERT: A 456 TYR cc_start: 0.8086 (t80) cc_final: 0.7712 (t80) REVERT: A 510 MET cc_start: 0.8395 (ttt) cc_final: 0.8134 (tpt) REVERT: A 511 LYS cc_start: 0.8577 (pptt) cc_final: 0.8249 (pttm) REVERT: A 647 MET cc_start: 0.8461 (tpt) cc_final: 0.8208 (tpt) REVERT: A 664 GLU cc_start: 0.8030 (tp30) cc_final: 0.7588 (tp30) REVERT: A 755 MET cc_start: 0.9061 (tpp) cc_final: 0.8796 (tpp) REVERT: A 1134 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 1147 ARG cc_start: 0.8184 (tpt90) cc_final: 0.7775 (mtp85) REVERT: A 1150 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7823 (tp30) REVERT: A 1154 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8164 (tp30) REVERT: A 1199 MET cc_start: 0.8413 (mmt) cc_final: 0.8006 (mmt) REVERT: A 1274 PHE cc_start: 0.9347 (t80) cc_final: 0.9135 (t80) REVERT: A 1276 TYR cc_start: 0.8319 (m-80) cc_final: 0.8002 (m-80) REVERT: A 1299 LEU cc_start: 0.8997 (mt) cc_final: 0.8650 (mt) REVERT: A 1300 HIS cc_start: 0.7881 (t-170) cc_final: 0.7551 (t70) REVERT: A 1301 ASN cc_start: 0.8971 (m-40) cc_final: 0.7971 (t0) REVERT: A 1312 ARG cc_start: 0.8258 (ttt90) cc_final: 0.7875 (mtp85) REVERT: A 1512 HIS cc_start: 0.6985 (m170) cc_final: 0.6585 (m-70) REVERT: A 1524 HIS cc_start: 0.8964 (m90) cc_final: 0.8533 (m-70) REVERT: B 43 GLU cc_start: 0.9122 (tt0) cc_final: 0.8705 (tp30) REVERT: B 48 TYR cc_start: 0.8686 (m-10) cc_final: 0.8318 (m-10) outliers start: 23 outliers final: 13 residues processed: 230 average time/residue: 0.0882 time to fit residues: 30.2195 Evaluate side-chains 214 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 90 optimal weight: 3.9990 chunk 139 optimal weight: 0.2980 chunk 89 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN A1524 HIS B 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.150454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106146 restraints weight = 22810.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106509 restraints weight = 13448.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108328 restraints weight = 9661.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108691 restraints weight = 7910.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108919 restraints weight = 7205.034| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.003 0.035 11734 Z= 0.134 Angle : 0.628 9.718 15843 Z= 0.307 Chirality : 0.040 0.189 1819 Planarity : 0.004 0.050 2001 Dihedral : 4.040 22.748 1557 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 1.81 % Allowed : 18.46 % Favored : 79.73 % 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: -0.24 (0.23), residues: 1426 helix: 1.49 (0.19), residues: 808 sheet: -0.81 (0.57), residues: 79 loop : -2.79 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 643 TYR 0.020 0.001 TYR A1503 PHE 0.036 0.001 PHE A1214 TRP 0.008 0.001 TRP A 325 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00300 (11725) covalent geometry : angle 0.62264 (15832) SS BOND : bond 0.00339 ( 1) SS BOND : angle 0.71820 ( 2) hydrogen bonds : bond 0.03374 ( 613) hydrogen bonds : angle 3.89654 ( 1785) metal coordination : bond 0.00855 ( 8) metal coordination : angle 3.42431 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6680 (mmt-90) REVERT: A 204 ASN cc_start: 0.8684 (p0) cc_final: 0.8477 (p0) REVERT: A 329 LEU cc_start: 0.8961 (mt) cc_final: 0.8739 (mt) REVERT: A 456 TYR cc_start: 0.8041 (t80) cc_final: 0.7689 (t80) REVERT: A 511 LYS cc_start: 0.8618 (pptt) cc_final: 0.8335 (pttm) REVERT: A 539 GLN cc_start: 0.7572 (tp40) cc_final: 0.6624 (mm-40) REVERT: A 598 THR cc_start: 0.9161 (p) cc_final: 0.8641 (t) REVERT: A 605 ASP cc_start: 0.8213 (t0) cc_final: 0.7930 (t0) REVERT: A 647 MET cc_start: 0.8459 (tpt) cc_final: 0.8187 (tpt) REVERT: A 664 GLU cc_start: 0.8078 (tp30) cc_final: 0.7601 (tp30) REVERT: A 755 MET cc_start: 0.8987 (tpp) cc_final: 0.8706 (tpp) REVERT: A 1120 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7831 (tttt) REVERT: A 1134 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 1147 ARG cc_start: 0.8124 (tpt90) cc_final: 0.7779 (mtp85) REVERT: A 1150 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7633 (tp30) REVERT: A 1154 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8248 (tp30) REVERT: A 1191 MET cc_start: 0.7829 (mtp) cc_final: 0.7148 (mpp) REVERT: A 1199 MET cc_start: 0.8407 (mmt) cc_final: 0.7978 (mmt) REVERT: A 1228 TYR cc_start: 0.7682 (m-80) cc_final: 0.7141 (m-80) REVERT: A 1274 PHE cc_start: 0.9269 (t80) cc_final: 0.9056 (t80) REVERT: A 1276 TYR cc_start: 0.8285 (m-80) cc_final: 0.7964 (m-80) REVERT: A 1299 LEU cc_start: 0.8978 (mt) cc_final: 0.8714 (mt) REVERT: A 1312 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7959 (mtp85) REVERT: A 1335 GLN cc_start: 0.7558 (pt0) cc_final: 0.7224 (pt0) REVERT: A 1388 ARG cc_start: 0.8310 (mmt90) cc_final: 0.7755 (ttm110) REVERT: A 1524 HIS cc_start: 0.8728 (m-70) cc_final: 0.8263 (m-70) REVERT: A 1654 ILE cc_start: 0.5704 (OUTLIER) cc_final: 0.5401 (pt) REVERT: B 43 GLU cc_start: 0.9099 (tt0) cc_final: 0.8608 (tp30) REVERT: B 48 TYR cc_start: 0.8569 (m-10) cc_final: 0.8136 (m-10) outliers start: 23 outliers final: 13 residues processed: 227 average time/residue: 0.0917 time to fit residues: 30.9397 Evaluate side-chains 211 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN A 738 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN A1530 ASN B 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.152152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108762 restraints weight = 22238.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108816 restraints weight = 12089.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.110415 restraints weight = 9084.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111451 restraints weight = 7400.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111548 restraints weight = 6657.032| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11734 Z= 0.106 Angle : 0.643 15.069 15843 Z= 0.307 Chirality : 0.040 0.206 1819 Planarity : 0.004 0.049 2001 Dihedral : 3.934 21.646 1557 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.65 % Allowed : 19.87 % Favored : 78.48 % 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: -0.04 (0.23), residues: 1426 helix: 1.62 (0.19), residues: 807 sheet: -0.78 (0.57), residues: 79 loop : -2.63 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1667 TYR 0.016 0.001 TYR A1125 PHE 0.041 0.001 PHE A1214 TRP 0.008 0.001 TRP A1549 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00228 (11725) covalent geometry : angle 0.63917 (15832) SS BOND : bond 0.00375 ( 1) SS BOND : angle 0.29937 ( 2) hydrogen bonds : bond 0.03124 ( 613) hydrogen bonds : angle 3.76830 ( 1785) metal coordination : bond 0.00291 ( 8) metal coordination : angle 3.08708 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6446 (mmt-90) REVERT: A 295 SER cc_start: 0.8322 (t) cc_final: 0.7547 (p) REVERT: A 329 LEU cc_start: 0.8853 (mt) cc_final: 0.8631 (mp) REVERT: A 456 TYR cc_start: 0.7909 (t80) cc_final: 0.7661 (t80) REVERT: A 511 LYS cc_start: 0.8659 (pptt) cc_final: 0.8378 (pttm) REVERT: A 539 GLN cc_start: 0.7419 (tp40) cc_final: 0.6337 (mm-40) REVERT: A 598 THR cc_start: 0.9159 (p) cc_final: 0.8635 (t) REVERT: A 647 MET cc_start: 0.8422 (tpt) cc_final: 0.8166 (tpt) REVERT: A 755 MET cc_start: 0.9040 (tpp) cc_final: 0.8726 (tpp) REVERT: A 1094 MET cc_start: 0.7030 (tpt) cc_final: 0.6352 (ppp) REVERT: A 1147 ARG cc_start: 0.8016 (tpt90) cc_final: 0.7704 (mtp85) REVERT: A 1150 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7724 (tp30) REVERT: A 1154 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8197 (tp30) REVERT: A 1191 MET cc_start: 0.7732 (mtp) cc_final: 0.6970 (mpp) REVERT: A 1199 MET cc_start: 0.8509 (mmt) cc_final: 0.8054 (mmt) REVERT: A 1228 TYR cc_start: 0.7607 (m-80) cc_final: 0.7248 (m-80) REVERT: A 1234 MET cc_start: 0.8523 (ttp) cc_final: 0.8185 (tmm) REVERT: A 1274 PHE cc_start: 0.9334 (t80) cc_final: 0.9078 (t80) REVERT: A 1276 TYR cc_start: 0.8325 (m-80) cc_final: 0.7963 (m-80) REVERT: A 1299 LEU cc_start: 0.8976 (mt) cc_final: 0.8696 (mt) REVERT: A 1312 ARG cc_start: 0.8254 (ttt90) cc_final: 0.7880 (mtp85) REVERT: A 1335 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: A 1441 LEU cc_start: 0.9074 (mt) cc_final: 0.8657 (mp) REVERT: A 1524 HIS cc_start: 0.8743 (m-70) cc_final: 0.8277 (m-70) REVERT: A 1654 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.5397 (pt) REVERT: B 43 GLU cc_start: 0.9064 (tt0) cc_final: 0.8619 (tp30) REVERT: B 48 TYR cc_start: 0.8617 (m-10) cc_final: 0.8279 (m-10) REVERT: B 69 MET cc_start: 0.8614 (tpp) cc_final: 0.8362 (mmm) outliers start: 21 outliers final: 13 residues processed: 225 average time/residue: 0.0891 time to fit residues: 29.7117 Evaluate side-chains 213 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1335 GLN Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 100 optimal weight: 0.1980 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN A1335 GLN ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 HIS A1556 HIS B 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.148839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104400 restraints weight = 22569.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.104797 restraints weight = 13566.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.105900 restraints weight = 9852.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107020 restraints weight = 8438.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107084 restraints weight = 7062.421| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11734 Z= 0.147 Angle : 0.665 11.566 15843 Z= 0.321 Chirality : 0.041 0.195 1819 Planarity : 0.004 0.048 2001 Dihedral : 4.024 22.447 1557 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.81 % Allowed : 20.42 % Favored : 77.77 % 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: -0.04 (0.23), residues: 1426 helix: 1.63 (0.19), residues: 801 sheet: -0.85 (0.57), residues: 84 loop : -2.60 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 435 TYR 0.016 0.001 TYR A1125 PHE 0.015 0.001 PHE A 541 TRP 0.008 0.001 TRP A1688 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00335 (11725) covalent geometry : angle 0.65904 (15832) SS BOND : bond 0.00394 ( 1) SS BOND : angle 0.50525 ( 2) hydrogen bonds : bond 0.03394 ( 613) hydrogen bonds : angle 3.89406 ( 1785) metal coordination : bond 0.01027 ( 8) metal coordination : angle 3.67126 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6947 (m-40) cc_final: 0.6258 (m-40) REVERT: A 185 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6474 (mmt-90) REVERT: A 329 LEU cc_start: 0.9042 (mt) cc_final: 0.8763 (mt) REVERT: A 456 TYR cc_start: 0.8014 (t80) cc_final: 0.7781 (t80) REVERT: A 539 GLN cc_start: 0.7729 (tp40) cc_final: 0.6766 (mm-40) REVERT: A 598 THR cc_start: 0.9184 (p) cc_final: 0.8643 (t) REVERT: A 647 MET cc_start: 0.8513 (tpt) cc_final: 0.8228 (tpt) REVERT: A 755 MET cc_start: 0.9046 (tpp) cc_final: 0.8759 (tpp) REVERT: A 1094 MET cc_start: 0.6973 (tpt) cc_final: 0.6388 (ppp) REVERT: A 1120 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7994 (tttt) REVERT: A 1147 ARG cc_start: 0.8022 (tpt90) cc_final: 0.7662 (mtp85) REVERT: A 1191 MET cc_start: 0.7787 (mtp) cc_final: 0.7197 (mpp) REVERT: A 1199 MET cc_start: 0.8524 (mmt) cc_final: 0.8105 (mmt) REVERT: A 1228 TYR cc_start: 0.7691 (m-80) cc_final: 0.7358 (m-80) REVERT: A 1234 MET cc_start: 0.8475 (ttp) cc_final: 0.8100 (tmm) REVERT: A 1276 TYR cc_start: 0.8312 (m-80) cc_final: 0.7980 (m-80) REVERT: A 1312 ARG cc_start: 0.8240 (ttt90) cc_final: 0.7876 (mtp85) REVERT: A 1388 ARG cc_start: 0.8338 (mmt90) cc_final: 0.7802 (ttm110) REVERT: A 1420 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 1524 HIS cc_start: 0.8729 (m-70) cc_final: 0.8239 (m-70) REVERT: B 43 GLU cc_start: 0.9094 (tt0) cc_final: 0.8670 (tp30) REVERT: B 48 TYR cc_start: 0.8635 (m-10) cc_final: 0.8208 (m-10) outliers start: 23 outliers final: 17 residues processed: 211 average time/residue: 0.0881 time to fit residues: 27.6887 Evaluate side-chains 209 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 104 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 126 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110655 restraints weight = 22382.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.111475 restraints weight = 13056.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112557 restraints weight = 9086.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.113755 restraints weight = 7908.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113736 restraints weight = 6580.763| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11734 Z= 0.110 Angle : 0.654 12.611 15843 Z= 0.312 Chirality : 0.040 0.189 1819 Planarity : 0.004 0.049 2001 Dihedral : 3.961 21.322 1557 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.65 % Allowed : 21.76 % Favored : 76.59 % 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: 0.13 (0.23), residues: 1426 helix: 1.79 (0.19), residues: 800 sheet: -0.83 (0.56), residues: 84 loop : -2.52 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 435 TYR 0.017 0.001 TYR A1125 PHE 0.043 0.001 PHE A1274 TRP 0.007 0.001 TRP A1549 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00242 (11725) covalent geometry : angle 0.64961 (15832) SS BOND : bond 0.00368 ( 1) SS BOND : angle 0.25789 ( 2) hydrogen bonds : bond 0.03139 ( 613) hydrogen bonds : angle 3.75248 ( 1785) metal coordination : bond 0.00414 ( 8) metal coordination : angle 3.11592 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7022 (m-40) cc_final: 0.6348 (m-40) REVERT: A 182 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7525 (pp20) REVERT: A 185 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6460 (mmt-90) REVERT: A 192 MET cc_start: 0.6380 (mmm) cc_final: 0.5576 (mmp) REVERT: A 295 SER cc_start: 0.8435 (t) cc_final: 0.7678 (p) REVERT: A 329 LEU cc_start: 0.8983 (mt) cc_final: 0.8656 (mp) REVERT: A 510 MET cc_start: 0.8445 (tpt) cc_final: 0.8161 (tpp) REVERT: A 539 GLN cc_start: 0.7539 (tp40) cc_final: 0.6556 (mm-40) REVERT: A 598 THR cc_start: 0.9130 (p) cc_final: 0.8592 (t) REVERT: A 621 LYS cc_start: 0.8942 (tttt) cc_final: 0.8578 (mtpt) REVERT: A 647 MET cc_start: 0.8371 (tpt) cc_final: 0.8138 (tpt) REVERT: A 665 GLU cc_start: 0.8521 (pt0) cc_final: 0.7822 (pt0) REVERT: A 671 GLU cc_start: 0.8263 (mp0) cc_final: 0.7809 (mp0) REVERT: A 755 MET cc_start: 0.8853 (tpp) cc_final: 0.8618 (tpp) REVERT: A 1094 MET cc_start: 0.6925 (tpt) cc_final: 0.6383 (ppp) REVERT: A 1147 ARG cc_start: 0.7906 (tpt90) cc_final: 0.7536 (mtp85) REVERT: A 1154 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8284 (tp30) REVERT: A 1191 MET cc_start: 0.7783 (mtp) cc_final: 0.7188 (mpp) REVERT: A 1199 MET cc_start: 0.8491 (mmt) cc_final: 0.8077 (mmt) REVERT: A 1228 TYR cc_start: 0.7637 (m-80) cc_final: 0.7317 (m-80) REVERT: A 1234 MET cc_start: 0.8436 (ttp) cc_final: 0.8217 (tmm) REVERT: A 1276 TYR cc_start: 0.8203 (m-80) cc_final: 0.7866 (m-80) REVERT: A 1312 ARG cc_start: 0.8213 (ttt90) cc_final: 0.7958 (mtp85) REVERT: A 1388 ARG cc_start: 0.8414 (mmt90) cc_final: 0.7923 (ttm110) REVERT: A 1420 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 1441 LEU cc_start: 0.9099 (mt) cc_final: 0.8740 (mp) REVERT: A 1524 HIS cc_start: 0.8604 (m-70) cc_final: 0.8180 (m-70) REVERT: B 43 GLU cc_start: 0.9052 (tt0) cc_final: 0.8591 (tp30) REVERT: B 48 TYR cc_start: 0.8481 (m-10) cc_final: 0.8122 (m-10) outliers start: 21 outliers final: 14 residues processed: 225 average time/residue: 0.0929 time to fit residues: 30.6280 Evaluate side-chains 217 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Chi-restraints excluded: chain B residue 62 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 0.0170 chunk 116 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 65 optimal weight: 0.0050 chunk 101 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 24 optimal weight: 5.9990 overall best weight: 0.1468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 290 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.154592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113181 restraints weight = 22209.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.114414 restraints weight = 12632.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115726 restraints weight = 8456.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116458 restraints weight = 7281.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.116685 restraints weight = 6095.905| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11734 Z= 0.111 Angle : 0.682 13.342 15843 Z= 0.320 Chirality : 0.040 0.215 1819 Planarity : 0.003 0.048 2001 Dihedral : 3.895 18.181 1557 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.49 % Allowed : 22.31 % Favored : 76.20 % 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: 0.23 (0.23), residues: 1426 helix: 1.85 (0.19), residues: 799 sheet: -0.72 (0.57), residues: 84 loop : -2.47 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 643 TYR 0.016 0.001 TYR A1125 PHE 0.041 0.001 PHE A1274 TRP 0.011 0.001 TRP A1549 HIS 0.005 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00234 (11725) covalent geometry : angle 0.67825 (15832) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.18145 ( 2) hydrogen bonds : bond 0.02997 ( 613) hydrogen bonds : angle 3.71787 ( 1785) metal coordination : bond 0.00229 ( 8) metal coordination : angle 2.90805 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6970 (m-40) cc_final: 0.6334 (m-40) REVERT: A 182 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: A 185 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6336 (mmt-90) REVERT: A 192 MET cc_start: 0.6460 (mmm) cc_final: 0.5814 (mmp) REVERT: A 295 SER cc_start: 0.8330 (t) cc_final: 0.7701 (p) REVERT: A 329 LEU cc_start: 0.8922 (mt) cc_final: 0.8675 (mp) REVERT: A 504 LEU cc_start: 0.9454 (tp) cc_final: 0.9219 (tp) REVERT: A 508 ASN cc_start: 0.8709 (m-40) cc_final: 0.8387 (m110) REVERT: A 539 GLN cc_start: 0.7318 (tp40) cc_final: 0.6384 (mm-40) REVERT: A 598 THR cc_start: 0.9129 (p) cc_final: 0.8608 (t) REVERT: A 647 MET cc_start: 0.8359 (tpt) cc_final: 0.8084 (tpt) REVERT: A 755 MET cc_start: 0.8935 (tpp) cc_final: 0.8663 (tpp) REVERT: A 1094 MET cc_start: 0.6956 (tpt) cc_final: 0.6433 (ppp) REVERT: A 1125 TYR cc_start: 0.7570 (p90) cc_final: 0.7029 (p90) REVERT: A 1147 ARG cc_start: 0.7756 (tpt90) cc_final: 0.7390 (mtp85) REVERT: A 1150 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7529 (tp30) REVERT: A 1154 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8217 (tp30) REVERT: A 1191 MET cc_start: 0.7828 (mtp) cc_final: 0.7576 (mtm) REVERT: A 1199 MET cc_start: 0.8593 (mmt) cc_final: 0.8249 (mmt) REVERT: A 1234 MET cc_start: 0.8509 (ttp) cc_final: 0.8222 (tmm) REVERT: A 1276 TYR cc_start: 0.8217 (m-80) cc_final: 0.7930 (m-80) REVERT: A 1278 ASN cc_start: 0.7861 (m-40) cc_final: 0.7278 (m-40) REVERT: A 1312 ARG cc_start: 0.8231 (ttt90) cc_final: 0.7947 (mtp85) REVERT: A 1441 LEU cc_start: 0.9050 (mt) cc_final: 0.8574 (mp) REVERT: A 1524 HIS cc_start: 0.8619 (m-70) cc_final: 0.8196 (m-70) REVERT: B 43 GLU cc_start: 0.8987 (tt0) cc_final: 0.8570 (tp30) REVERT: B 48 TYR cc_start: 0.8526 (m-10) cc_final: 0.8245 (m-10) outliers start: 19 outliers final: 14 residues processed: 236 average time/residue: 0.0873 time to fit residues: 30.7618 Evaluate side-chains 219 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Chi-restraints excluded: chain A residue 1785 CYS Chi-restraints excluded: chain B residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1408 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104862 restraints weight = 22329.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105911 restraints weight = 13475.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106805 restraints weight = 9410.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108079 restraints weight = 8236.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108245 restraints weight = 6835.239| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11734 Z= 0.132 Angle : 0.726 15.232 15843 Z= 0.342 Chirality : 0.041 0.203 1819 Planarity : 0.004 0.047 2001 Dihedral : 3.982 21.276 1557 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.57 % Allowed : 23.88 % Favored : 74.55 % 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: 0.19 (0.23), residues: 1426 helix: 1.85 (0.19), residues: 800 sheet: -0.85 (0.57), residues: 84 loop : -2.51 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 643 TYR 0.017 0.001 TYR A1125 PHE 0.045 0.002 PHE A1274 TRP 0.008 0.001 TRP A1471 HIS 0.006 0.001 HIS A1287 Details of bonding type rmsd covalent geometry : bond 0.00302 (11725) covalent geometry : angle 0.72190 (15832) SS BOND : bond 0.00316 ( 1) SS BOND : angle 0.36972 ( 2) hydrogen bonds : bond 0.03227 ( 613) hydrogen bonds : angle 3.84611 ( 1785) metal coordination : bond 0.00840 ( 8) metal coordination : angle 3.43683 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6923 (m-40) cc_final: 0.6288 (m-40) REVERT: A 182 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7574 (pp20) REVERT: A 185 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6339 (mmt-90) REVERT: A 295 SER cc_start: 0.8435 (t) cc_final: 0.7654 (p) REVERT: A 329 LEU cc_start: 0.8899 (mt) cc_final: 0.8625 (mp) REVERT: A 539 GLN cc_start: 0.7690 (tp40) cc_final: 0.6721 (mm-40) REVERT: A 598 THR cc_start: 0.9173 (p) cc_final: 0.8707 (t) REVERT: A 619 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8512 (mm) REVERT: A 647 MET cc_start: 0.8537 (tpt) cc_final: 0.8225 (tpt) REVERT: A 755 MET cc_start: 0.9047 (tpp) cc_final: 0.8774 (tpt) REVERT: A 1094 MET cc_start: 0.6933 (tpt) cc_final: 0.6469 (ppp) REVERT: A 1147 ARG cc_start: 0.7864 (tpt90) cc_final: 0.7452 (mtp85) REVERT: A 1150 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7789 (tp30) REVERT: A 1154 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8338 (tp30) REVERT: A 1191 MET cc_start: 0.7896 (mtp) cc_final: 0.7540 (mtm) REVERT: A 1199 MET cc_start: 0.8455 (mmt) cc_final: 0.8239 (mmt) REVERT: A 1205 PHE cc_start: 0.8471 (m-80) cc_final: 0.8195 (m-80) REVERT: A 1234 MET cc_start: 0.8542 (ttp) cc_final: 0.8276 (tmm) REVERT: A 1240 MET cc_start: 0.6978 (mpt) cc_final: 0.6531 (mtt) REVERT: A 1276 TYR cc_start: 0.8379 (m-80) cc_final: 0.8063 (m-80) REVERT: A 1278 ASN cc_start: 0.7913 (m-40) cc_final: 0.7438 (m110) REVERT: A 1294 MET cc_start: 0.6964 (ttp) cc_final: 0.6725 (ttt) REVERT: A 1312 ARG cc_start: 0.8339 (ttt90) cc_final: 0.7930 (mtp85) REVERT: A 1388 ARG cc_start: 0.8421 (mmt90) cc_final: 0.7827 (ttm110) REVERT: A 1441 LEU cc_start: 0.9059 (mt) cc_final: 0.8628 (mp) REVERT: A 1524 HIS cc_start: 0.8718 (m-70) cc_final: 0.8244 (m-70) REVERT: B 43 GLU cc_start: 0.9101 (tt0) cc_final: 0.8602 (tp30) REVERT: B 48 TYR cc_start: 0.8546 (m-10) cc_final: 0.8186 (m-10) REVERT: B 68 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8693 (mtmm) REVERT: B 69 MET cc_start: 0.8542 (tpt) cc_final: 0.8237 (tpp) outliers start: 20 outliers final: 16 residues processed: 215 average time/residue: 0.0858 time to fit residues: 27.7799 Evaluate side-chains 214 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Chi-restraints excluded: chain A residue 1785 CYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 14 optimal weight: 0.0070 chunk 63 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 141 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1408 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106590 restraints weight = 22489.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107598 restraints weight = 13346.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108859 restraints weight = 9226.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109585 restraints weight = 8002.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109749 restraints weight = 6732.289| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11734 Z= 0.118 Angle : 0.740 14.776 15843 Z= 0.344 Chirality : 0.041 0.200 1819 Planarity : 0.003 0.047 2001 Dihedral : 3.939 19.156 1557 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.65 % Allowed : 23.88 % Favored : 74.47 % 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: 0.24 (0.23), residues: 1426 helix: 1.88 (0.19), residues: 800 sheet: -0.85 (0.57), residues: 82 loop : -2.47 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 643 TYR 0.015 0.001 TYR A1125 PHE 0.050 0.001 PHE A1274 TRP 0.006 0.001 TRP A1549 HIS 0.003 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00264 (11725) covalent geometry : angle 0.73630 (15832) SS BOND : bond 0.00327 ( 1) SS BOND : angle 0.19199 ( 2) hydrogen bonds : bond 0.03097 ( 613) hydrogen bonds : angle 3.79960 ( 1785) metal coordination : bond 0.00336 ( 8) metal coordination : angle 3.13769 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.6934 (m-40) cc_final: 0.6329 (m-40) REVERT: A 182 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7530 (pp20) REVERT: A 185 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6372 (mmt-90) REVERT: A 295 SER cc_start: 0.8330 (t) cc_final: 0.7604 (p) REVERT: A 329 LEU cc_start: 0.8844 (mt) cc_final: 0.8597 (mp) REVERT: A 508 ASN cc_start: 0.8849 (m-40) cc_final: 0.8525 (m110) REVERT: A 539 GLN cc_start: 0.7481 (tp40) cc_final: 0.6541 (mm-40) REVERT: A 598 THR cc_start: 0.9171 (p) cc_final: 0.8695 (t) REVERT: A 622 MET cc_start: 0.8127 (mpp) cc_final: 0.7895 (mpp) REVERT: A 647 MET cc_start: 0.8479 (tpt) cc_final: 0.8181 (tpt) REVERT: A 755 MET cc_start: 0.9069 (tpp) cc_final: 0.8830 (tpp) REVERT: A 1094 MET cc_start: 0.6826 (tpt) cc_final: 0.6449 (ppp) REVERT: A 1125 TYR cc_start: 0.7723 (p90) cc_final: 0.7176 (p90) REVERT: A 1147 ARG cc_start: 0.7828 (tpt90) cc_final: 0.7469 (mtp85) REVERT: A 1150 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7733 (tp30) REVERT: A 1154 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8369 (tp30) REVERT: A 1199 MET cc_start: 0.8588 (mmt) cc_final: 0.8346 (mmt) REVERT: A 1234 MET cc_start: 0.8417 (ttp) cc_final: 0.8110 (tmm) REVERT: A 1240 MET cc_start: 0.6895 (mpt) cc_final: 0.6553 (mtt) REVERT: A 1242 GLU cc_start: 0.7839 (tt0) cc_final: 0.7378 (tt0) REVERT: A 1276 TYR cc_start: 0.8414 (m-80) cc_final: 0.8128 (m-80) REVERT: A 1278 ASN cc_start: 0.7883 (m-40) cc_final: 0.7450 (m110) REVERT: A 1312 ARG cc_start: 0.8299 (ttt90) cc_final: 0.7988 (mtp85) REVERT: A 1388 ARG cc_start: 0.8422 (mmt90) cc_final: 0.7841 (ttm110) REVERT: A 1441 LEU cc_start: 0.9031 (mt) cc_final: 0.8564 (mp) REVERT: A 1524 HIS cc_start: 0.8708 (m-70) cc_final: 0.8077 (m-70) REVERT: B 43 GLU cc_start: 0.9095 (tt0) cc_final: 0.8600 (tp30) REVERT: B 48 TYR cc_start: 0.8593 (m-10) cc_final: 0.8312 (m-10) REVERT: B 68 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8621 (mtmm) REVERT: B 69 MET cc_start: 0.8439 (tpt) cc_final: 0.8105 (tpp) outliers start: 21 outliers final: 13 residues processed: 225 average time/residue: 0.0816 time to fit residues: 27.4840 Evaluate side-chains 218 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1645 GLN Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1783 ASP Chi-restraints excluded: chain B residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 114 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1408 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1504 ASN B 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112354 restraints weight = 22611.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110465 restraints weight = 12368.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112515 restraints weight = 9798.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.112879 restraints weight = 7491.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113051 restraints weight = 6841.944| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11734 Z= 0.124 Angle : 0.741 14.461 15843 Z= 0.346 Chirality : 0.041 0.196 1819 Planarity : 0.003 0.047 2001 Dihedral : 3.960 19.949 1557 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.49 % Allowed : 24.51 % Favored : 74.00 % 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: 0.28 (0.23), residues: 1426 helix: 1.88 (0.19), residues: 799 sheet: -0.78 (0.59), residues: 77 loop : -2.39 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 643 TYR 0.055 0.001 TYR A1152 PHE 0.051 0.001 PHE A1274 TRP 0.006 0.001 TRP A1666 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00280 (11725) covalent geometry : angle 0.73754 (15832) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.31752 ( 2) hydrogen bonds : bond 0.03201 ( 613) hydrogen bonds : angle 3.84883 ( 1785) metal coordination : bond 0.00504 ( 8) metal coordination : angle 3.24563 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2043.94 seconds wall clock time: 36 minutes 8.10 seconds (2168.10 seconds total)