Starting phenix.real_space_refine on Fri Sep 11 19:38:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6klc_0706/09_2026/6klc_0706.cif" } resolution = 3.9 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 72 5.16 5 C 7134 2.51 5 N 1866 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11210 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11209 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 41, 'TRANS': 1394} Chain breaks: 18 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 343 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 13, 'PHE:plan': 9, 'GLN:plan1': 4, 'TRP:plan': 2, 'TYR:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.23 Number of scatterers: 11210 At special positions: 0 Unit cell: (119.68, 112.88, 125.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 72 16.00 O 2137 8.00 N 1866 7.00 C 7134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 617.8 milliseconds 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 58.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 removed outlier: 3.603A pdb=" N ILE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.997A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 170 through 177 removed outlier: 4.282A pdb=" N SER A 174 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 232 through 249 removed outlier: 3.884A pdb=" N LEU A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.896A pdb=" N PHE A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.533A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 removed outlier: 4.241A pdb=" N MET A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.530A pdb=" N ARG A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 411 No H-bonds generated for 'chain 'A' and resid 410 through 411' Processing helix chain 'A' and resid 415 through 415 No H-bonds generated for 'chain 'A' and resid 415 through 415' Processing helix chain 'A' and resid 416 through 436 removed outlier: 3.560A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.725A pdb=" N ARG A 581 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 583 " --> pdb=" O LYS A 580 " (cutoff:3.500A) Proline residue: A 584 - end of helix Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.564A pdb=" N GLN A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.791A pdb=" N LEU A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 709 Processing helix chain 'A' and resid 717 through 737 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.555A 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 846 through 862 Processing helix chain 'A' and resid 870 through 886 removed outlier: 3.640A pdb=" N LEU A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 912 through 929 removed outlier: 3.563A pdb=" N GLU A 929 " --> pdb=" O ASP A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1098 removed outlier: 4.004A pdb=" N LEU A1098 " --> pdb=" O MET A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1159 Processing helix chain 'A' and resid 1167 through 1184 removed outlier: 3.608A pdb=" N MET A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1211 removed outlier: 3.532A pdb=" N PHE A1205 " --> pdb=" O CYS A1201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1238 removed outlier: 3.848A pdb=" N LEU A1229 " --> pdb=" O GLY A1225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A1238 " --> pdb=" O MET A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1270 through 1282 removed outlier: 3.646A pdb=" N GLY A1282 " --> pdb=" O ASN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 removed outlier: 3.515A pdb=" N THR A1344 " --> pdb=" O ASP A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.642A pdb=" N PHE A1354 " --> pdb=" O ASP A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1408 removed outlier: 4.173A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1432 Processing helix chain 'A' and resid 1435 through 1452 removed outlier: 3.975A 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 1506 removed outlier: 3.593A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1518 removed outlier: 4.395A pdb=" N PHE A1515 " --> pdb=" O LEU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 4.232A pdb=" N LYS A1584 " --> pdb=" O PRO A1580 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A1590 " --> pdb=" O ILE A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 removed outlier: 3.670A pdb=" N GLY A1618 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1619 " --> pdb=" O ILE A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1649 removed outlier: 3.773A pdb=" N ILE A1644 " --> pdb=" O TYR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1742 through 1752 Processing helix chain 'A' and resid 1781 through 1788 Processing helix chain 'A' and resid 1797 through 1802 removed outlier: 3.807A pdb=" N VAL A1802 " --> pdb=" O VAL A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1820 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.003A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 100 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.557A pdb=" N PHE A 541 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1121 through 1126 removed outlier: 3.548A pdb=" N ARG A1133 " --> pdb=" O LYS A1126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1326 through 1330 removed outlier: 3.894A pdb=" N GLY A1379 " --> pdb=" O SER A1188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1241 through 1242 Processing sheet with id=AA6, first strand: chain 'A' and resid 1382 through 1385 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AA8, first strand: chain 'A' and resid 1631 through 1632 600 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2957 1.33 - 1.45: 1968 1.45 - 1.57: 6361 1.57 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 11395 Sorted by residual: bond pdb=" N ASP A1334 " pdb=" CA ASP A1334 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.89e+00 bond pdb=" C VAL A1434 " pdb=" O VAL A1434 " ideal model delta sigma weight residual 1.240 1.213 0.027 1.26e-02 6.30e+03 4.48e+00 bond pdb=" N TYR A1452 " pdb=" CA TYR A1452 " ideal model delta sigma weight residual 1.458 1.430 0.027 1.33e-02 5.65e+03 4.12e+00 bond pdb=" CA ILE A 152 " pdb=" CB ILE A 152 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" C TYR A1455 " pdb=" O TYR A1455 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.72e+00 ... (remaining 11390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14610 1.41 - 2.82: 659 2.82 - 4.22: 99 4.22 - 5.63: 31 5.63 - 7.04: 11 Bond angle restraints: 15410 Sorted by residual: angle pdb=" C TYR A1455 " pdb=" N PRO A1456 " pdb=" CA PRO A1456 " ideal model delta sigma weight residual 119.84 126.53 -6.69 1.25e+00 6.40e-01 2.86e+01 angle pdb=" N VAL A 690 " pdb=" CA VAL A 690 " pdb=" C VAL A 690 " ideal model delta sigma weight residual 113.47 108.15 5.32 1.01e+00 9.80e-01 2.78e+01 angle pdb=" N VAL A1436 " pdb=" CA VAL A1436 " pdb=" C VAL A1436 " ideal model delta sigma weight residual 110.36 115.66 -5.30 1.05e+00 9.07e-01 2.54e+01 angle pdb=" N THR A1116 " pdb=" CA THR A1116 " pdb=" C THR A1116 " ideal model delta sigma weight residual 114.04 109.13 4.91 1.24e+00 6.50e-01 1.56e+01 angle pdb=" N TYR A1665 " pdb=" CA TYR A1665 " pdb=" C TYR A1665 " ideal model delta sigma weight residual 108.13 114.23 -6.10 1.72e+00 3.38e-01 1.26e+01 ... (remaining 15405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 6309 17.59 - 35.19: 506 35.19 - 52.78: 85 52.78 - 70.37: 13 70.37 - 87.96: 6 Dihedral angle restraints: 6919 sinusoidal: 2698 harmonic: 4221 Sorted by residual: dihedral pdb=" CA ARG A 336 " pdb=" C ARG A 336 " pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR A 706 " pdb=" C TYR A 706 " pdb=" N MET A 707 " pdb=" CA MET A 707 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ALA A 744 " pdb=" C ALA A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1653 0.071 - 0.143: 145 0.143 - 0.214: 10 0.214 - 0.286: 1 0.286 - 0.357: 1 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CA HIS A 443 " pdb=" N HIS A 443 " pdb=" C HIS A 443 " pdb=" CB HIS A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA HIS A1437 " pdb=" N HIS A1437 " pdb=" C HIS A1437 " pdb=" CB HIS A1437 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN A1432 " pdb=" N ASN A1432 " pdb=" C ASN A1432 " pdb=" CB ASN A1432 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 1807 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1431 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ALA A1431 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A1431 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN A1432 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1333 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASP A1333 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A1333 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A1334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 152 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 153 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.029 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1013 2.74 - 3.28: 11920 3.28 - 3.82: 17702 3.82 - 4.36: 20024 4.36 - 4.90: 34375 Nonbonded interactions: 85034 Sorted by model distance: nonbonded pdb=" O PRO A1459 " pdb=" NE2 GLN A1483 " model vdw 2.198 3.120 nonbonded pdb=" OE2 GLU A 731 " pdb=" OG1 THR A1271 " model vdw 2.217 3.040 nonbonded pdb=" O SER A 440 " pdb=" OG SER A 440 " model vdw 2.222 3.040 nonbonded pdb=" OD2 ASP A 89 " pdb=" N CYS A 103 " model vdw 2.281 3.120 nonbonded pdb=" NH1 ARG A 643 " pdb=" OH TYR A 706 " model vdw 2.282 3.120 ... (remaining 85029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11395 Z= 0.168 Angle : 0.700 7.040 15410 Z= 0.426 Chirality : 0.043 0.357 1810 Planarity : 0.003 0.053 1949 Dihedral : 13.241 87.964 4165 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.30 % Favored : 90.49 % Rotamer: Outliers : 0.64 % Allowed : 5.06 % Favored : 94.30 % 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: -3.27 (0.19), residues: 1398 helix: -1.02 (0.16), residues: 789 sheet: -1.64 (0.49), residues: 108 loop : -4.21 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 643 TYR 0.014 0.001 TYR A 706 PHE 0.011 0.001 PHE A 104 TRP 0.007 0.001 TRP A1704 HIS 0.005 0.001 HIS A 738 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (11395) covalent geometry : angle 0.70029 / 0.43 (15410) hydrogen bonds : bond 0.12718 / 9.03 ( 600) hydrogen bonds : angle 6.69663 / 4.62 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 359 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.5901 (ttm) cc_final: 0.5571 (ttm) REVERT: A 113 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 114 GLN cc_start: 0.7941 (tp40) cc_final: 0.7684 (tt0) REVERT: A 115 LYS cc_start: 0.8040 (tptt) cc_final: 0.7423 (tptt) REVERT: A 118 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6421 (tm-30) REVERT: A 240 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 241 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 325 TRP cc_start: 0.7701 (m100) cc_final: 0.7179 (m100) REVERT: A 407 MET cc_start: 0.8844 (mmp) cc_final: 0.8114 (mmt) REVERT: A 448 MET cc_start: 0.7376 (tmm) cc_final: 0.7106 (tmm) REVERT: A 660 ASP cc_start: 0.7612 (t0) cc_final: 0.7253 (t0) REVERT: A 727 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 856 LEU cc_start: 0.9525 (tp) cc_final: 0.8910 (tp) REVERT: A 860 PHE cc_start: 0.7793 (m-80) cc_final: 0.7425 (m-80) REVERT: A 925 ASP cc_start: 0.8953 (t0) cc_final: 0.8688 (t0) REVERT: A 926 GLN cc_start: 0.9020 (pp30) cc_final: 0.8733 (pp30) REVERT: A 1094 MET cc_start: 0.3657 (pmm) cc_final: 0.3317 (pmm) REVERT: A 1151 ASP cc_start: 0.8649 (p0) cc_final: 0.8420 (p0) REVERT: A 1160 LEU cc_start: 0.9142 (mt) cc_final: 0.8917 (mp) REVERT: A 1242 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 1253 LYS cc_start: 0.8353 (tptp) cc_final: 0.8041 (mmtt) REVERT: A 1341 GLN cc_start: 0.8304 (pp30) cc_final: 0.7747 (pp30) REVERT: A 1364 MET cc_start: 0.7935 (mmm) cc_final: 0.7593 (tpp) REVERT: A 1436 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 1479 ARG cc_start: 0.7935 (mtt90) cc_final: 0.6928 (mtm180) REVERT: A 1485 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8210 (mm-30) REVERT: A 1551 ASN cc_start: 0.7951 (t0) cc_final: 0.7448 (t0) REVERT: A 1629 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7901 (mmtp) REVERT: A 1797 LEU cc_start: 0.6333 (mt) cc_final: 0.5891 (mm) outliers start: 8 outliers final: 5 residues processed: 365 average time/residue: 0.1171 time to fit residues: 59.9917 Evaluate side-chains 252 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 246 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1457 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.4705 > 50:) chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 ASN A 289 HIS A 758 ASN A 794 ASN A 869 ASN A1128 GLN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 HIS A1287 HIS A1315 ASN A1409 ASN A1451 GLN A1475 ASN A1551 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.157376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118271 restraints weight = 20455.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121712 restraints weight = 12386.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124067 restraints weight = 8801.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125563 restraints weight = 6961.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126447 restraints weight = 5975.167| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11395 Z= 0.143 Angle : 0.680 9.550 15410 Z= 0.345 Chirality : 0.043 0.303 1810 Planarity : 0.004 0.040 1949 Dihedral : 5.280 53.559 1528 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.73 % Favored : 90.20 % Rotamer: Outliers : 2.73 % Allowed : 15.42 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.21), residues: 1398 helix: 0.15 (0.18), residues: 802 sheet: -1.18 (0.50), residues: 110 loop : -3.93 (0.22), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 697 TYR 0.017 0.001 TYR A1665 PHE 0.018 0.002 PHE A1402 TRP 0.013 0.001 TRP A 155 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (11395) covalent geometry : angle 0.67977 / 0.35 (15410) hydrogen bonds : bond 0.04341 / 2.98 ( 600) hydrogen bonds : angle 4.56964 / 3.18 ( 1752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6145 (ttm) cc_final: 0.5804 (ttm) REVERT: A 113 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 115 LYS cc_start: 0.8209 (tptt) cc_final: 0.7636 (tptt) REVERT: A 118 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6620 (tm-30) REVERT: A 240 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 241 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 323 GLN cc_start: 0.8727 (mp10) cc_final: 0.8492 (mp10) REVERT: A 325 TRP cc_start: 0.7663 (m100) cc_final: 0.7414 (m100) REVERT: A 335 MET cc_start: 0.7914 (pmm) cc_final: 0.7521 (pmm) REVERT: A 360 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.5886 (pp30) REVERT: A 407 MET cc_start: 0.8896 (mmp) cc_final: 0.8466 (mmt) REVERT: A 657 ASP cc_start: 0.7157 (t0) cc_final: 0.6659 (t0) REVERT: A 660 ASP cc_start: 0.7399 (t0) cc_final: 0.6968 (t0) REVERT: A 727 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 733 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8609 (mptt) REVERT: A 752 LEU cc_start: 0.9211 (mt) cc_final: 0.8991 (mt) REVERT: A 856 LEU cc_start: 0.9546 (tp) cc_final: 0.8888 (tp) REVERT: A 860 PHE cc_start: 0.7894 (m-80) cc_final: 0.7482 (m-80) REVERT: A 881 MET cc_start: 0.8322 (mtm) cc_final: 0.7945 (mtm) REVERT: A 889 LYS cc_start: 0.7314 (mptt) cc_final: 0.7095 (mptt) REVERT: A 925 ASP cc_start: 0.8887 (t0) cc_final: 0.8667 (t0) REVERT: A 926 GLN cc_start: 0.8990 (pp30) cc_final: 0.8754 (pp30) REVERT: A 1094 MET cc_start: 0.3866 (pmm) cc_final: 0.3412 (pmm) REVERT: A 1151 ASP cc_start: 0.8765 (p0) cc_final: 0.8471 (p0) REVERT: A 1240 MET cc_start: 0.6273 (ttm) cc_final: 0.5651 (tmm) REVERT: A 1242 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7032 (mm-30) REVERT: A 1253 LYS cc_start: 0.8358 (tptp) cc_final: 0.8127 (mmtt) REVERT: A 1341 GLN cc_start: 0.8112 (pp30) cc_final: 0.7544 (pp30) REVERT: A 1364 MET cc_start: 0.7995 (mmm) cc_final: 0.7792 (mmt) REVERT: A 1454 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8154 (mmp-170) REVERT: A 1460 PHE cc_start: 0.8577 (m-10) cc_final: 0.8350 (m-80) REVERT: A 1479 ARG cc_start: 0.7792 (mtt90) cc_final: 0.7239 (mtt180) REVERT: A 1485 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 1551 ASN cc_start: 0.8075 (t0) cc_final: 0.7450 (t0) REVERT: A 1629 LYS cc_start: 0.8450 (mmtt) cc_final: 0.7948 (mmtp) outliers start: 34 outliers final: 18 residues processed: 302 average time/residue: 0.0989 time to fit residues: 44.2865 Evaluate side-chains 268 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1623 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN A1236 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN A1664 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116936 restraints weight = 20622.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120326 restraints weight = 12403.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122614 restraints weight = 8846.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124150 restraints weight = 7046.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124893 restraints weight = 6029.000| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11395 Z= 0.144 Angle : 0.674 10.219 15410 Z= 0.340 Chirality : 0.044 0.246 1810 Planarity : 0.004 0.039 1949 Dihedral : 5.232 53.531 1525 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.94 % Favored : 89.99 % Rotamer: Outliers : 3.78 % Allowed : 16.47 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.22), residues: 1398 helix: 0.73 (0.18), residues: 797 sheet: -0.77 (0.50), residues: 107 loop : -3.67 (0.23), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 336 TYR 0.019 0.001 TYR A1665 PHE 0.015 0.001 PHE A 799 TRP 0.010 0.001 TRP A 155 HIS 0.003 0.001 HIS A1186 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11395) covalent geometry : angle 0.67369 / 0.34 (15410) hydrogen bonds : bond 0.04143 / 2.83 ( 600) hydrogen bonds : angle 4.28017 / 2.98 ( 1752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.500 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 40 MET cc_start: 0.6192 (ttm) cc_final: 0.5800 (ttm) REVERT: A 113 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7122 (mm-30) REVERT: A 114 GLN cc_start: 0.7693 (pt0) cc_final: 0.7026 (pp30) REVERT: A 115 LYS cc_start: 0.8206 (tptt) cc_final: 0.7865 (tptt) REVERT: A 118 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6691 (tp30) REVERT: A 240 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 302 TYR cc_start: 0.8050 (m-80) cc_final: 0.7838 (m-80) REVERT: A 407 MET cc_start: 0.8880 (mmp) cc_final: 0.8557 (mmt) REVERT: A 657 ASP cc_start: 0.7115 (t0) cc_final: 0.6628 (t0) REVERT: A 660 ASP cc_start: 0.7422 (t0) cc_final: 0.7006 (t0) REVERT: A 727 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 856 LEU cc_start: 0.9544 (tp) cc_final: 0.8852 (tp) REVERT: A 860 PHE cc_start: 0.8139 (m-80) cc_final: 0.7706 (m-80) REVERT: A 881 MET cc_start: 0.8286 (mtm) cc_final: 0.7898 (mtm) REVERT: A 1094 MET cc_start: 0.4176 (pmm) cc_final: 0.3713 (pmm) REVERT: A 1151 ASP cc_start: 0.8793 (p0) cc_final: 0.8476 (p0) REVERT: A 1253 LYS cc_start: 0.8427 (tptp) cc_final: 0.8210 (mmtt) REVERT: A 1301 ASN cc_start: 0.8560 (m110) cc_final: 0.8269 (m-40) REVERT: A 1341 GLN cc_start: 0.8041 (pp30) cc_final: 0.7476 (pp30) REVERT: A 1344 THR cc_start: 0.9134 (p) cc_final: 0.8922 (t) REVERT: A 1364 MET cc_start: 0.8207 (mmm) cc_final: 0.7976 (mmt) REVERT: A 1479 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7489 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 1551 ASN cc_start: 0.8103 (t0) cc_final: 0.7503 (t0) REVERT: A 1560 MET cc_start: 0.8687 (ptp) cc_final: 0.8212 (mtt) REVERT: A 1629 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7910 (mmtp) REVERT: A 1688 TRP cc_start: 0.7555 (t60) cc_final: 0.7322 (t-100) outliers start: 47 outliers final: 29 residues processed: 290 average time/residue: 0.0952 time to fit residues: 41.3087 Evaluate side-chains 275 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1623 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113287 restraints weight = 20910.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116628 restraints weight = 12739.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118810 restraints weight = 9155.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120209 restraints weight = 7353.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121029 restraints weight = 6344.427| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11395 Z= 0.176 Angle : 0.707 13.075 15410 Z= 0.356 Chirality : 0.045 0.345 1810 Planarity : 0.004 0.038 1949 Dihedral : 4.966 28.126 1518 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.09 % Favored : 89.84 % Rotamer: Outliers : 3.78 % Allowed : 18.39 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1398 helix: 0.82 (0.18), residues: 805 sheet: -0.66 (0.50), residues: 107 loop : -3.51 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 336 TYR 0.023 0.001 TYR A1665 PHE 0.014 0.002 PHE A 423 TRP 0.018 0.001 TRP A 325 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (11395) covalent geometry : angle 0.70700 / 0.36 (15410) hydrogen bonds : bond 0.04330 / 2.95 ( 600) hydrogen bonds : angle 4.33740 / 3.01 ( 1752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 0.453 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 113 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7263 (mt-10) REVERT: A 114 GLN cc_start: 0.7706 (pt0) cc_final: 0.7318 (pp30) REVERT: A 115 LYS cc_start: 0.8237 (tptt) cc_final: 0.7553 (tmtt) REVERT: A 325 TRP cc_start: 0.7634 (m100) cc_final: 0.7297 (m100) REVERT: A 388 LYS cc_start: 0.8337 (mptt) cc_final: 0.7765 (mptt) REVERT: A 407 MET cc_start: 0.8915 (mmp) cc_final: 0.8692 (mmt) REVERT: A 660 ASP cc_start: 0.7528 (t0) cc_final: 0.7296 (t0) REVERT: A 661 LYS cc_start: 0.8239 (tptt) cc_final: 0.8026 (tptm) REVERT: A 727 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 856 LEU cc_start: 0.9545 (tp) cc_final: 0.8934 (tp) REVERT: A 860 PHE cc_start: 0.8130 (m-80) cc_final: 0.7729 (m-80) REVERT: A 881 MET cc_start: 0.8345 (mtm) cc_final: 0.7922 (mtm) REVERT: A 917 LYS cc_start: 0.9284 (mmmt) cc_final: 0.8898 (mmmt) REVERT: A 925 ASP cc_start: 0.8948 (t0) cc_final: 0.8727 (t0) REVERT: A 926 GLN cc_start: 0.9050 (pp30) cc_final: 0.8787 (pp30) REVERT: A 1094 MET cc_start: 0.4071 (pmm) cc_final: 0.3643 (pmm) REVERT: A 1151 ASP cc_start: 0.8817 (p0) cc_final: 0.8513 (p0) REVERT: A 1226 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7040 (ttm170) REVERT: A 1240 MET cc_start: 0.6811 (ttp) cc_final: 0.6446 (ttp) REVERT: A 1301 ASN cc_start: 0.8652 (m110) cc_final: 0.8383 (m-40) REVERT: A 1341 GLN cc_start: 0.8137 (pp30) cc_final: 0.7512 (pp30) REVERT: A 1344 THR cc_start: 0.9275 (p) cc_final: 0.9068 (t) REVERT: A 1364 MET cc_start: 0.8273 (mmm) cc_final: 0.8025 (mmt) REVERT: A 1479 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7516 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8207 (mt-10) REVERT: A 1551 ASN cc_start: 0.8287 (t0) cc_final: 0.7781 (t0) REVERT: A 1560 MET cc_start: 0.8703 (ptp) cc_final: 0.8251 (mtt) REVERT: A 1629 LYS cc_start: 0.8577 (mmtt) cc_final: 0.7948 (mmtp) outliers start: 47 outliers final: 34 residues processed: 286 average time/residue: 0.0968 time to fit residues: 41.2987 Evaluate side-chains 272 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1623 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN A 593 GLN A1110 ASN ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.155399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116591 restraints weight = 20545.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120034 restraints weight = 12305.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122356 restraints weight = 8736.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123807 restraints weight = 6934.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124525 restraints weight = 5942.427| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11395 Z= 0.129 Angle : 0.688 13.162 15410 Z= 0.342 Chirality : 0.045 0.364 1810 Planarity : 0.004 0.038 1949 Dihedral : 4.802 23.984 1518 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.51 % Favored : 90.41 % Rotamer: Outliers : 3.78 % Allowed : 20.00 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1398 helix: 1.02 (0.18), residues: 804 sheet: -0.45 (0.51), residues: 107 loop : -3.43 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 336 TYR 0.016 0.001 TYR A1665 PHE 0.014 0.001 PHE A 423 TRP 0.010 0.001 TRP A1688 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11395) covalent geometry : angle 0.68785 / 0.34 (15410) hydrogen bonds : bond 0.03970 / 2.72 ( 600) hydrogen bonds : angle 4.12010 / 2.87 ( 1752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 0.458 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 91 TYR cc_start: 0.4317 (p90) cc_final: 0.3989 (p90) REVERT: A 113 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7442 (mt-10) REVERT: A 115 LYS cc_start: 0.8107 (tptt) cc_final: 0.7220 (tmtt) REVERT: A 325 TRP cc_start: 0.7752 (m100) cc_final: 0.7442 (m100) REVERT: A 407 MET cc_start: 0.8868 (mmp) cc_final: 0.8505 (mmt) REVERT: A 493 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8936 (m) REVERT: A 578 ASP cc_start: 0.7900 (t0) cc_final: 0.7399 (m-30) REVERT: A 602 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: A 657 ASP cc_start: 0.7272 (t0) cc_final: 0.6742 (t0) REVERT: A 660 ASP cc_start: 0.7576 (t0) cc_final: 0.7164 (t0) REVERT: A 661 LYS cc_start: 0.8240 (tptt) cc_final: 0.7956 (tptm) REVERT: A 727 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 856 LEU cc_start: 0.9529 (tp) cc_final: 0.8859 (tp) REVERT: A 860 PHE cc_start: 0.8127 (m-80) cc_final: 0.7751 (m-80) REVERT: A 917 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8855 (mmmt) REVERT: A 925 ASP cc_start: 0.8902 (t0) cc_final: 0.8678 (t0) REVERT: A 926 GLN cc_start: 0.9053 (pp30) cc_final: 0.8819 (pp30) REVERT: A 1094 MET cc_start: 0.4359 (pmm) cc_final: 0.4081 (ptt) REVERT: A 1151 ASP cc_start: 0.8787 (p0) cc_final: 0.8471 (p0) REVERT: A 1226 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6965 (ttm170) REVERT: A 1242 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 1252 MET cc_start: 0.8535 (mmm) cc_final: 0.8334 (mmm) REVERT: A 1301 ASN cc_start: 0.8626 (m110) cc_final: 0.8332 (m-40) REVERT: A 1338 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8896 (mt) REVERT: A 1341 GLN cc_start: 0.8179 (pp30) cc_final: 0.7556 (pp30) REVERT: A 1344 THR cc_start: 0.9289 (p) cc_final: 0.9079 (t) REVERT: A 1364 MET cc_start: 0.8264 (mmm) cc_final: 0.7856 (tpp) REVERT: A 1479 ARG cc_start: 0.7926 (mtt90) cc_final: 0.7443 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 1551 ASN cc_start: 0.8256 (t0) cc_final: 0.7756 (t0) REVERT: A 1560 MET cc_start: 0.8708 (ptp) cc_final: 0.8230 (mtt) REVERT: A 1629 LYS cc_start: 0.8528 (mmtt) cc_final: 0.7872 (mmtp) outliers start: 47 outliers final: 30 residues processed: 283 average time/residue: 0.0952 time to fit residues: 40.4623 Evaluate side-chains 271 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1527 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.153714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114055 restraints weight = 20931.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117426 restraints weight = 12729.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119584 restraints weight = 9168.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121151 restraints weight = 7354.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122010 restraints weight = 6323.700| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11395 Z= 0.153 Angle : 0.692 13.007 15410 Z= 0.348 Chirality : 0.044 0.353 1810 Planarity : 0.004 0.038 1949 Dihedral : 4.826 25.394 1518 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.16 % Favored : 89.77 % Rotamer: Outliers : 3.86 % Allowed : 21.45 % Favored : 74.70 % 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: -0.83 (0.23), residues: 1398 helix: 1.02 (0.18), residues: 804 sheet: -0.27 (0.52), residues: 101 loop : -3.44 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 336 TYR 0.020 0.001 TYR A1665 PHE 0.014 0.001 PHE A 423 TRP 0.009 0.001 TRP A 155 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (11395) covalent geometry : angle 0.69240 / 0.35 (15410) hydrogen bonds : bond 0.04062 / 2.75 ( 600) hydrogen bonds : angle 4.17089 / 2.91 ( 1752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.443 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 91 TYR cc_start: 0.4405 (p90) cc_final: 0.4145 (p90) REVERT: A 115 LYS cc_start: 0.8110 (tptt) cc_final: 0.7155 (tmtt) REVERT: A 302 TYR cc_start: 0.8361 (m-80) cc_final: 0.8136 (m-80) REVERT: A 325 TRP cc_start: 0.8061 (m100) cc_final: 0.7714 (m100) REVERT: A 388 LYS cc_start: 0.8334 (mptt) cc_final: 0.7746 (mptt) REVERT: A 407 MET cc_start: 0.8889 (mmp) cc_final: 0.8523 (mmt) REVERT: A 435 ARG cc_start: 0.8396 (tpm170) cc_final: 0.7836 (ttm-80) REVERT: A 493 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8732 (m) REVERT: A 602 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: A 657 ASP cc_start: 0.7084 (t0) cc_final: 0.6558 (t0) REVERT: A 660 ASP cc_start: 0.7647 (t0) cc_final: 0.7254 (t0) REVERT: A 727 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 856 LEU cc_start: 0.9530 (tp) cc_final: 0.8880 (tp) REVERT: A 860 PHE cc_start: 0.8203 (m-80) cc_final: 0.7807 (m-80) REVERT: A 917 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8842 (mmmt) REVERT: A 925 ASP cc_start: 0.8913 (t0) cc_final: 0.8694 (t0) REVERT: A 1094 MET cc_start: 0.4414 (pmm) cc_final: 0.4144 (ptt) REVERT: A 1151 ASP cc_start: 0.8743 (p0) cc_final: 0.8422 (p0) REVERT: A 1226 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7031 (ttm170) REVERT: A 1240 MET cc_start: 0.6971 (ttp) cc_final: 0.6685 (ptt) REVERT: A 1251 MET cc_start: 0.8117 (mmm) cc_final: 0.7733 (tpt) REVERT: A 1252 MET cc_start: 0.8483 (mmm) cc_final: 0.8040 (mmm) REVERT: A 1301 ASN cc_start: 0.8655 (m110) cc_final: 0.8363 (m-40) REVERT: A 1338 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8907 (mt) REVERT: A 1341 GLN cc_start: 0.8136 (pp30) cc_final: 0.7407 (pp30) REVERT: A 1344 THR cc_start: 0.9211 (p) cc_final: 0.9009 (t) REVERT: A 1479 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7540 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 1551 ASN cc_start: 0.8290 (t0) cc_final: 0.7853 (t0) REVERT: A 1560 MET cc_start: 0.8712 (ptp) cc_final: 0.8243 (mtt) REVERT: A 1629 LYS cc_start: 0.8558 (mmtt) cc_final: 0.7913 (mmtp) outliers start: 48 outliers final: 37 residues processed: 273 average time/residue: 0.0952 time to fit residues: 38.9530 Evaluate side-chains 277 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1693 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 86 optimal weight: 0.0770 chunk 128 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 0.0370 chunk 116 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117326 restraints weight = 20738.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120809 restraints weight = 12455.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123102 restraints weight = 8887.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124639 restraints weight = 7078.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125529 restraints weight = 6078.368| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11395 Z= 0.123 Angle : 0.697 13.172 15410 Z= 0.347 Chirality : 0.044 0.354 1810 Planarity : 0.004 0.040 1949 Dihedral : 4.690 23.411 1518 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.87 % Favored : 91.06 % Rotamer: Outliers : 2.89 % Allowed : 22.73 % Favored : 74.38 % 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: -0.70 (0.23), residues: 1398 helix: 1.12 (0.18), residues: 807 sheet: -0.33 (0.50), residues: 107 loop : -3.41 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 336 TYR 0.014 0.001 TYR A1665 PHE 0.015 0.001 PHE A 423 TRP 0.019 0.001 TRP A1549 HIS 0.003 0.000 HIS A1287 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11395) covalent geometry : angle 0.69703 / 0.35 (15410) hydrogen bonds : bond 0.03763 / 2.55 ( 600) hydrogen bonds : angle 4.01800 / 2.82 ( 1752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.459 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 41 GLU cc_start: 0.8200 (mp0) cc_final: 0.7826 (pm20) REVERT: A 91 TYR cc_start: 0.4328 (p90) cc_final: 0.4067 (p90) REVERT: A 115 LYS cc_start: 0.8124 (tptt) cc_final: 0.7186 (tmtt) REVERT: A 325 TRP cc_start: 0.8020 (m100) cc_final: 0.7807 (m100) REVERT: A 407 MET cc_start: 0.8632 (mmp) cc_final: 0.8408 (mmt) REVERT: A 435 ARG cc_start: 0.8364 (tpm170) cc_final: 0.7764 (ttm-80) REVERT: A 493 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8720 (m) REVERT: A 578 ASP cc_start: 0.7805 (t0) cc_final: 0.7307 (m-30) REVERT: A 602 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.8240 (m-10) REVERT: A 657 ASP cc_start: 0.7180 (t0) cc_final: 0.6648 (t0) REVERT: A 660 ASP cc_start: 0.7650 (t0) cc_final: 0.7278 (t0) REVERT: A 698 PHE cc_start: 0.8920 (t80) cc_final: 0.8682 (t80) REVERT: A 727 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 856 LEU cc_start: 0.9510 (tp) cc_final: 0.8792 (tp) REVERT: A 860 PHE cc_start: 0.8203 (m-80) cc_final: 0.7806 (m-80) REVERT: A 917 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8824 (mmmt) REVERT: A 925 ASP cc_start: 0.8922 (t0) cc_final: 0.8698 (t0) REVERT: A 926 GLN cc_start: 0.9069 (pp30) cc_final: 0.8570 (pp30) REVERT: A 1094 MET cc_start: 0.4450 (pmm) cc_final: 0.4235 (ptp) REVERT: A 1252 MET cc_start: 0.8320 (mmm) cc_final: 0.7906 (mmm) REVERT: A 1301 ASN cc_start: 0.8578 (m110) cc_final: 0.8317 (m-40) REVERT: A 1338 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8856 (mt) REVERT: A 1341 GLN cc_start: 0.8105 (pp30) cc_final: 0.7476 (pp30) REVERT: A 1364 MET cc_start: 0.8335 (mmt) cc_final: 0.8070 (mmt) REVERT: A 1460 PHE cc_start: 0.8254 (m-80) cc_final: 0.7799 (m-80) REVERT: A 1479 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7507 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8192 (mt-10) REVERT: A 1551 ASN cc_start: 0.8131 (t0) cc_final: 0.7637 (t0) outliers start: 36 outliers final: 28 residues processed: 268 average time/residue: 0.0950 time to fit residues: 38.4576 Evaluate side-chains 260 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1797 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 0.0020 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 overall best weight: 0.7548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117506 restraints weight = 20624.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120976 restraints weight = 12478.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123244 restraints weight = 8907.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124699 restraints weight = 7105.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125821 restraints weight = 6108.851| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11395 Z= 0.129 Angle : 0.719 16.327 15410 Z= 0.358 Chirality : 0.045 0.330 1810 Planarity : 0.003 0.040 1949 Dihedral : 4.633 23.932 1517 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer: Outliers : 3.21 % Allowed : 23.21 % Favored : 73.57 % 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: -0.66 (0.23), residues: 1398 helix: 1.17 (0.18), residues: 806 sheet: -0.36 (0.50), residues: 107 loop : -3.40 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 336 TYR 0.022 0.001 TYR A 552 PHE 0.013 0.001 PHE A 423 TRP 0.008 0.001 TRP A 155 HIS 0.007 0.001 HIS A1287 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (11395) covalent geometry : angle 0.71916 / 0.36 (15410) hydrogen bonds : bond 0.03766 / 2.56 ( 600) hydrogen bonds : angle 3.99069 / 2.79 ( 1752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 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 41 GLU cc_start: 0.8369 (mp0) cc_final: 0.8016 (pm20) REVERT: A 91 TYR cc_start: 0.4514 (p90) cc_final: 0.4306 (p90) REVERT: A 115 LYS cc_start: 0.8111 (tptt) cc_final: 0.7184 (tmtt) REVERT: A 325 TRP cc_start: 0.8106 (m100) cc_final: 0.7856 (m100) REVERT: A 407 MET cc_start: 0.8638 (mmp) cc_final: 0.8412 (mmt) REVERT: A 435 ARG cc_start: 0.8338 (tpm170) cc_final: 0.7732 (ttm-80) REVERT: A 493 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8646 (m) REVERT: A 510 MET cc_start: 0.8289 (tpp) cc_final: 0.8089 (tpp) REVERT: A 578 ASP cc_start: 0.7886 (t0) cc_final: 0.7331 (m-30) REVERT: A 602 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: A 657 ASP cc_start: 0.7214 (t0) cc_final: 0.6664 (t0) REVERT: A 660 ASP cc_start: 0.7690 (t0) cc_final: 0.7325 (t0) REVERT: A 727 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 856 LEU cc_start: 0.9507 (tp) cc_final: 0.8744 (tp) REVERT: A 860 PHE cc_start: 0.8194 (m-80) cc_final: 0.7795 (m-80) REVERT: A 917 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8814 (mmmt) REVERT: A 926 GLN cc_start: 0.9088 (pp30) cc_final: 0.8812 (pp30) REVERT: A 1151 ASP cc_start: 0.8700 (p0) cc_final: 0.8358 (p0) REVERT: A 1252 MET cc_start: 0.8277 (mmm) cc_final: 0.7899 (mmm) REVERT: A 1301 ASN cc_start: 0.8587 (m110) cc_final: 0.8313 (m-40) REVERT: A 1338 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8850 (mt) REVERT: A 1341 GLN cc_start: 0.8107 (pp30) cc_final: 0.7403 (pp30) REVERT: A 1364 MET cc_start: 0.8151 (mmt) cc_final: 0.7682 (mmt) REVERT: A 1479 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7524 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 1551 ASN cc_start: 0.8192 (t0) cc_final: 0.7718 (t0) REVERT: A 1750 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7138 (tmt-80) outliers start: 40 outliers final: 33 residues processed: 262 average time/residue: 0.0950 time to fit residues: 37.7611 Evaluate side-chains 267 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1693 ILE Chi-restraints excluded: chain A residue 1797 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 8.9990 chunk 139 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116619 restraints weight = 20579.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118841 restraints weight = 12746.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120717 restraints weight = 8809.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121699 restraints weight = 7280.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121633 restraints weight = 6545.675| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11395 Z= 0.161 Angle : 0.756 16.747 15410 Z= 0.377 Chirality : 0.045 0.351 1810 Planarity : 0.004 0.039 1949 Dihedral : 4.739 23.265 1517 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.73 % Favored : 90.20 % Rotamer: Outliers : 3.21 % Allowed : 23.69 % Favored : 73.09 % 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: -0.68 (0.23), residues: 1398 helix: 1.13 (0.18), residues: 808 sheet: -0.46 (0.51), residues: 100 loop : -3.33 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 336 TYR 0.019 0.001 TYR A 552 PHE 0.016 0.002 PHE A1203 TRP 0.008 0.001 TRP A 155 HIS 0.011 0.001 HIS A1287 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11395) covalent geometry : angle 0.75606 / 0.38 (15410) hydrogen bonds : bond 0.04015 / 2.74 ( 600) hydrogen bonds : angle 4.16716 / 2.91 ( 1752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.468 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 40 MET cc_start: 0.7856 (mpp) cc_final: 0.6982 (ptm) REVERT: A 323 GLN cc_start: 0.8422 (mp10) cc_final: 0.8135 (pm20) REVERT: A 325 TRP cc_start: 0.8168 (m100) cc_final: 0.7862 (m100) REVERT: A 388 LYS cc_start: 0.8390 (mptt) cc_final: 0.7861 (mptt) REVERT: A 407 MET cc_start: 0.8767 (mmp) cc_final: 0.8496 (mmt) REVERT: A 435 ARG cc_start: 0.8524 (tpm170) cc_final: 0.7916 (ttm-80) REVERT: A 448 MET cc_start: 0.8014 (mtt) cc_final: 0.7665 (tmm) REVERT: A 493 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8729 (m) REVERT: A 578 ASP cc_start: 0.7932 (t0) cc_final: 0.7404 (m-30) REVERT: A 602 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.8174 (m-10) REVERT: A 657 ASP cc_start: 0.7429 (t0) cc_final: 0.6797 (t0) REVERT: A 660 ASP cc_start: 0.7878 (t0) cc_final: 0.7531 (t0) REVERT: A 661 LYS cc_start: 0.8291 (tptt) cc_final: 0.8044 (tptm) REVERT: A 727 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 856 LEU cc_start: 0.9519 (tp) cc_final: 0.8794 (tp) REVERT: A 860 PHE cc_start: 0.8008 (m-80) cc_final: 0.7667 (m-80) REVERT: A 917 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8805 (mmmt) REVERT: A 926 GLN cc_start: 0.9086 (pp30) cc_final: 0.8868 (pp30) REVERT: A 1251 MET cc_start: 0.8228 (mmm) cc_final: 0.7876 (tpt) REVERT: A 1252 MET cc_start: 0.8366 (mmm) cc_final: 0.8016 (mmm) REVERT: A 1253 LYS cc_start: 0.9049 (mptt) cc_final: 0.8618 (mttt) REVERT: A 1301 ASN cc_start: 0.8688 (m110) cc_final: 0.8407 (m-40) REVERT: A 1338 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 1341 GLN cc_start: 0.8121 (pp30) cc_final: 0.7290 (pp30) REVERT: A 1364 MET cc_start: 0.8333 (mmt) cc_final: 0.8053 (mmt) REVERT: A 1479 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7551 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 1551 ASN cc_start: 0.8195 (t0) cc_final: 0.7743 (t0) outliers start: 40 outliers final: 34 residues processed: 253 average time/residue: 0.0916 time to fit residues: 35.0611 Evaluate side-chains 262 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1797 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 69 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 126 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.157261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118218 restraints weight = 20639.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121755 restraints weight = 12435.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124062 restraints weight = 8822.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125634 restraints weight = 6986.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126580 restraints weight = 5977.817| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11395 Z= 0.129 Angle : 0.771 17.112 15410 Z= 0.376 Chirality : 0.046 0.367 1810 Planarity : 0.003 0.039 1949 Dihedral : 4.689 23.189 1517 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.80 % Favored : 91.13 % Rotamer: Outliers : 2.97 % Allowed : 24.34 % Favored : 72.69 % 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: -0.59 (0.23), residues: 1398 helix: 1.19 (0.18), residues: 809 sheet: -0.42 (0.51), residues: 98 loop : -3.25 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 336 TYR 0.017 0.001 TYR A 552 PHE 0.013 0.001 PHE A1305 TRP 0.009 0.001 TRP A1549 HIS 0.008 0.001 HIS A1287 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (11395) covalent geometry : angle 0.77104 / 0.38 (15410) hydrogen bonds : bond 0.03762 / 2.57 ( 600) hydrogen bonds : angle 4.03901 / 2.82 ( 1752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.501 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 40 MET cc_start: 0.7715 (mpp) cc_final: 0.6981 (ptm) REVERT: A 325 TRP cc_start: 0.8035 (m100) cc_final: 0.7792 (m100) REVERT: A 407 MET cc_start: 0.8681 (mmp) cc_final: 0.8458 (mmt) REVERT: A 435 ARG cc_start: 0.8346 (tpm170) cc_final: 0.7812 (ttm-80) REVERT: A 493 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8627 (m) REVERT: A 578 ASP cc_start: 0.7836 (t0) cc_final: 0.7336 (m-30) REVERT: A 602 TRP cc_start: 0.8853 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: A 657 ASP cc_start: 0.7244 (t0) cc_final: 0.6691 (t0) REVERT: A 660 ASP cc_start: 0.7664 (t0) cc_final: 0.7313 (t0) REVERT: A 661 LYS cc_start: 0.8163 (tptt) cc_final: 0.7924 (tptm) REVERT: A 727 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 856 LEU cc_start: 0.9513 (tp) cc_final: 0.8859 (tp) REVERT: A 860 PHE cc_start: 0.7946 (m-80) cc_final: 0.7660 (m-80) REVERT: A 917 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8769 (mmmt) REVERT: A 1199 MET cc_start: 0.8507 (mmp) cc_final: 0.8230 (mmt) REVERT: A 1237 MET cc_start: 0.8133 (mmt) cc_final: 0.7835 (mmt) REVERT: A 1252 MET cc_start: 0.8264 (mmm) cc_final: 0.7954 (mmm) REVERT: A 1253 LYS cc_start: 0.9058 (mptt) cc_final: 0.8614 (mttt) REVERT: A 1301 ASN cc_start: 0.8607 (m110) cc_final: 0.8359 (m-40) REVERT: A 1338 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8860 (mt) REVERT: A 1341 GLN cc_start: 0.7995 (pp30) cc_final: 0.7209 (pp30) REVERT: A 1364 MET cc_start: 0.8337 (mmt) cc_final: 0.8065 (mmt) REVERT: A 1479 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7520 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 1502 LEU cc_start: 0.8850 (tp) cc_final: 0.8366 (pp) REVERT: A 1519 TYR cc_start: 0.7389 (t80) cc_final: 0.6297 (t80) REVERT: A 1551 ASN cc_start: 0.8240 (t0) cc_final: 0.7810 (t0) outliers start: 37 outliers final: 29 residues processed: 254 average time/residue: 0.0956 time to fit residues: 36.3455 Evaluate side-chains 258 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1797 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.152869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113731 restraints weight = 20816.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117108 restraints weight = 12627.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119226 restraints weight = 9042.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120775 restraints weight = 7288.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121708 restraints weight = 6232.171| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11395 Z= 0.174 Angle : 0.796 16.933 15410 Z= 0.395 Chirality : 0.047 0.358 1810 Planarity : 0.004 0.051 1949 Dihedral : 4.829 22.905 1517 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.37 % Favored : 89.56 % Rotamer: Outliers : 2.97 % Allowed : 24.58 % Favored : 72.45 % 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: -0.69 (0.23), residues: 1398 helix: 1.12 (0.18), residues: 809 sheet: -0.48 (0.52), residues: 94 loop : -3.31 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 336 TYR 0.020 0.001 TYR A1665 PHE 0.016 0.002 PHE A1460 TRP 0.009 0.001 TRP A 155 HIS 0.010 0.001 HIS A1287 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (11395) covalent geometry : angle 0.79589 / 0.39 (15410) hydrogen bonds : bond 0.04160 / 2.84 ( 600) hydrogen bonds : angle 4.24014 / 2.96 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.43 seconds wall clock time: 36 minutes 24.31 seconds (2184.31 seconds total)