Starting phenix.real_space_refine on Thu Jun 4 07:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vs4_65296/06_2026/9vs4_65296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vs4_65296/06_2026/9vs4_65296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vs4_65296/06_2026/9vs4_65296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vs4_65296/06_2026/9vs4_65296.map" model { file = "/net/cci-nas-00/data/ceres_data/9vs4_65296/06_2026/9vs4_65296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vs4_65296/06_2026/9vs4_65296.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 7155 2.51 5 N 1831 2.21 5 O 2071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11134 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 11032 Classifications: {'peptide': 1360} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 1310} Chain breaks: 11 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'SVR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'SVR:plan-3': 1, 'SVR:plan-4': 1, 'SVR:plan-7': 1, 'SVR:plan-9': 1, 'SVR:plan-1': 1, 'SVR:plan-8': 1, 'SVR:plan-10': 1, 'SVR:plan-11': 1} Unresolved non-hydrogen planarities: 66 Time building chain proxies: 2.35, per 1000 atoms: 0.21 Number of scatterers: 11134 At special positions: 0 Unit cell: (95.95, 102.6, 114.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2071 8.00 N 1831 7.00 C 7155 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 432.2 milliseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 11 sheets defined 59.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.586A pdb=" N LEU A 201 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.513A pdb=" N LYS A 300 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.608A pdb=" N LEU A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 447 through 465 Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 502 through 522 removed outlier: 3.683A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.733A pdb=" N ILE A 571 " --> pdb=" O ARG A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 607 through 621 removed outlier: 3.631A pdb=" N LEU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.539A pdb=" N VAL A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 662 Proline residue: A 652 - end of helix removed outlier: 4.748A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 681 through 701 Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 738 through 753 Proline residue: A 749 - end of helix removed outlier: 3.540A pdb=" N PHE A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN A 753 " --> pdb=" O PRO A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 796 through 815 removed outlier: 4.296A pdb=" N ARG A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 941 removed outlier: 3.716A pdb=" N LYS A 939 " --> pdb=" O MET A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 984 removed outlier: 3.971A pdb=" N VAL A 975 " --> pdb=" O CYS A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1024 removed outlier: 3.905A pdb=" N ARG A1000 " --> pdb=" O ASP A 996 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1056 removed outlier: 3.983A pdb=" N TRP A1052 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1076 Processing helix chain 'A' and resid 1083 through 1090 Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1125 through 1150 Processing helix chain 'A' and resid 1178 through 1197 removed outlier: 3.531A pdb=" N PHE A1197 " --> pdb=" O VAL A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1234 removed outlier: 3.612A pdb=" N LEU A1233 " --> pdb=" O TYR A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1262 Processing helix chain 'A' and resid 1265 through 1283 Processing helix chain 'A' and resid 1317 through 1324 Processing helix chain 'A' and resid 1327 through 1342 removed outlier: 3.671A pdb=" N LYS A1340 " --> pdb=" O ASN A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1347 removed outlier: 3.724A pdb=" N GLN A1347 " --> pdb=" O LEU A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1356 removed outlier: 3.795A pdb=" N THR A1356 " --> pdb=" O GLN A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1379 removed outlier: 3.527A pdb=" N PHE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1416 removed outlier: 3.696A pdb=" N LEU A1414 " --> pdb=" O THR A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1429 removed outlier: 3.787A pdb=" N MET A1427 " --> pdb=" O PHE A1423 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A1428 " --> pdb=" O LYS A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1452 through 1463 Processing helix chain 'A' and resid 1466 through 1474 removed outlier: 3.634A pdb=" N SER A1474 " --> pdb=" O LYS A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1488 Processing helix chain 'A' and resid 1523 through 1538 removed outlier: 3.560A pdb=" N GLN A1537 " --> pdb=" O ARG A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 removed outlier: 3.535A pdb=" N VAL A1553 " --> pdb=" O PHE A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1569 removed outlier: 3.585A pdb=" N CYS A1569 " --> pdb=" O THR A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1598 through 1608 Processing helix chain 'A' and resid 1616 through 1635 removed outlier: 3.686A pdb=" N LEU A1620 " --> pdb=" O ASP A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1646 removed outlier: 3.691A pdb=" N ASN A1646 " --> pdb=" O MET A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1675 removed outlier: 4.096A pdb=" N LEU A1657 " --> pdb=" O GLY A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1705 Processing sheet with id=AA1, first strand: chain 'A' and resid 293 through 295 removed outlier: 5.687A pdb=" N GLU A 293 " --> pdb=" O ILE A 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.432A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE A 561 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.432A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 664 through 665 removed outlier: 3.620A pdb=" N SER A 664 " --> pdb=" O ILE A1208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 728 through 729 Processing sheet with id=AA7, first strand: chain 'A' and resid 843 through 846 Processing sheet with id=AA8, first strand: chain 'A' and resid 963 through 964 removed outlier: 6.578A pdb=" N PHE A 946 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A1078 " --> pdb=" O ILE A1116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AB1, first strand: chain 'A' and resid 1571 through 1576 removed outlier: 4.803A pdb=" N ALA A1573 " --> pdb=" O THR A1713 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A1713 " --> pdb=" O ALA A1573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1581 through 1584 602 hydrogen bonds defined for protein. 1746 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: 2.13 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2048 1.33 - 1.45: 2860 1.45 - 1.58: 6334 1.58 - 1.70: 1 1.70 - 1.83: 123 Bond restraints: 11366 Sorted by residual: bond pdb=" C VAL A1684 " pdb=" O VAL A1684 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.79e+00 bond pdb=" C PRO A 440 " pdb=" O PRO A 440 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.16e-02 7.43e+03 7.51e+00 bond pdb=" N VAL A1682 " pdb=" CA VAL A1682 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.20e-02 6.94e+03 6.95e+00 bond pdb=" N LYS A 441 " pdb=" CA LYS A 441 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.22e-02 6.72e+03 5.58e+00 bond pdb=" C LYS A1683 " pdb=" O LYS A1683 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.21e-02 6.83e+03 5.55e+00 ... (remaining 11361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 15210 2.95 - 5.90: 133 5.90 - 8.85: 19 8.85 - 11.79: 5 11.79 - 14.74: 2 Bond angle restraints: 15369 Sorted by residual: angle pdb=" CA PRO A 476 " pdb=" N PRO A 476 " pdb=" CD PRO A 476 " ideal model delta sigma weight residual 112.00 104.24 7.76 1.40e+00 5.10e-01 3.07e+01 angle pdb=" CB MET A1295 " pdb=" CG MET A1295 " pdb=" SD MET A1295 " ideal model delta sigma weight residual 112.70 127.44 -14.74 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CB MET A 656 " pdb=" CG MET A 656 " pdb=" SD MET A 656 " ideal model delta sigma weight residual 112.70 98.64 14.06 3.00e+00 1.11e-01 2.20e+01 angle pdb=" CA LYS A1683 " pdb=" C LYS A1683 " pdb=" O LYS A1683 " ideal model delta sigma weight residual 120.43 115.91 4.52 1.09e+00 8.42e-01 1.72e+01 angle pdb=" C VAL A1684 " pdb=" N PHE A1685 " pdb=" CA PHE A1685 " ideal model delta sigma weight residual 122.72 128.36 -5.64 1.38e+00 5.25e-01 1.67e+01 ... (remaining 15364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5692 17.10 - 34.21: 906 34.21 - 51.31: 212 51.31 - 68.41: 40 68.41 - 85.51: 16 Dihedral angle restraints: 6866 sinusoidal: 2822 harmonic: 4044 Sorted by residual: dihedral pdb=" CA PRO A 476 " pdb=" C PRO A 476 " pdb=" N ILE A 477 " pdb=" CA ILE A 477 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA MET A 937 " pdb=" C MET A 937 " pdb=" N MET A 938 " pdb=" CA MET A 938 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A 478 " pdb=" C ILE A 478 " pdb=" N SER A 479 " pdb=" CA SER A 479 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1354 0.052 - 0.104: 310 0.104 - 0.156: 46 0.156 - 0.207: 7 0.207 - 0.259: 4 Chirality restraints: 1721 Sorted by residual: chirality pdb=" CA LYS A1683 " pdb=" N LYS A1683 " pdb=" C LYS A1683 " pdb=" CB LYS A1683 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL A1684 " pdb=" N VAL A1684 " pdb=" C VAL A1684 " pdb=" CB VAL A1684 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB THR A 456 " pdb=" CA THR A 456 " pdb=" OG1 THR A 456 " pdb=" CG2 THR A 456 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1718 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 475 " 0.056 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 476 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 340 " -0.021 2.00e-02 2.50e+03 1.92e-02 9.18e+00 pdb=" CG TRP A 340 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 340 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 340 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 340 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 340 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 340 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 340 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 340 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 409 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C GLN A 409 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN A 409 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 410 " -0.017 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 306 2.70 - 3.25: 11140 3.25 - 3.80: 19049 3.80 - 4.35: 24304 4.35 - 4.90: 40756 Nonbonded interactions: 95555 Sorted by model distance: nonbonded pdb=" OE1 GLU A 293 " pdb=" CD LYS A 441 " model vdw 2.156 3.440 nonbonded pdb=" OH TYR A1496 " pdb=" OD2 ASP A1534 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A1419 " pdb=" OH TYR A1464 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A1319 " pdb=" OG1 THR A1565 " model vdw 2.269 3.040 nonbonded pdb=" O ILE A 477 " pdb=" OG SER A1274 " model vdw 2.270 3.040 ... (remaining 95550 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 11367 Z= 0.188 Angle : 0.746 14.743 15369 Z= 0.390 Chirality : 0.046 0.259 1721 Planarity : 0.005 0.080 1926 Dihedral : 17.535 85.513 4228 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.88 % Allowed : 27.79 % Favored : 71.33 % 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: -0.21 (0.22), residues: 1336 helix: 0.34 (0.18), residues: 738 sheet: -0.58 (0.64), residues: 68 loop : -0.61 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 825 TYR 0.017 0.002 TYR A 670 PHE 0.030 0.002 PHE A 675 TRP 0.050 0.002 TRP A 340 HIS 0.008 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (11366) covalent geometry : angle 0.74630 / 0.39 (15369) hydrogen bonds : bond 0.14259 / 8.64 ( 593) hydrogen bonds : angle 5.68911 / 4.07 ( 1746) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.5842 (mtp) cc_final: 0.5455 (ptp) REVERT: A 293 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 588 PHE cc_start: 0.7780 (m-80) cc_final: 0.7326 (m-80) REVERT: A 644 LYS cc_start: 0.6687 (pttm) cc_final: 0.6072 (pmtt) REVERT: A 664 SER cc_start: 0.8611 (p) cc_final: 0.8406 (t) REVERT: A 788 LYS cc_start: 0.7457 (mmtt) cc_final: 0.7256 (mmpt) REVERT: A 1010 ILE cc_start: 0.6743 (mt) cc_final: 0.6414 (mt) REVERT: A 1149 LYS cc_start: 0.7098 (ttmm) cc_final: 0.6376 (ptpt) REVERT: A 1181 MET cc_start: 0.6988 (mtm) cc_final: 0.6463 (mtm) REVERT: A 1182 ILE cc_start: 0.8090 (mm) cc_final: 0.7878 (mm) REVERT: A 1344 LEU cc_start: 0.7851 (mt) cc_final: 0.7633 (tm) REVERT: A 1467 LYS cc_start: 0.6341 (mmtp) cc_final: 0.5072 (ttpt) REVERT: A 1530 MET cc_start: 0.6683 (mtm) cc_final: 0.6462 (mtp) REVERT: A 1681 LYS cc_start: 0.7165 (tttt) cc_final: 0.6401 (ttmm) outliers start: 11 outliers final: 3 residues processed: 191 average time/residue: 0.5519 time to fit residues: 113.9707 Evaluate side-chains 158 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 1588 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 461 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1124 ASN A1210 HIS A1330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112567 restraints weight = 13223.766| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.83 r_work: 0.3193 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11367 Z= 0.218 Angle : 0.613 8.145 15369 Z= 0.316 Chirality : 0.042 0.157 1721 Planarity : 0.004 0.051 1926 Dihedral : 6.349 75.436 1472 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.82 % Allowed : 25.38 % Favored : 69.80 % 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: 0.30 (0.22), residues: 1336 helix: 0.84 (0.18), residues: 751 sheet: -0.33 (0.62), residues: 77 loop : -0.56 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 825 TYR 0.025 0.002 TYR A 670 PHE 0.025 0.002 PHE A 418 TRP 0.022 0.002 TRP A 340 HIS 0.009 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (11366) covalent geometry : angle 0.61285 / 0.32 (15369) hydrogen bonds : bond 0.04503 / 2.94 ( 593) hydrogen bonds : angle 4.44075 / 3.19 ( 1746) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7758 (p0) REVERT: A 293 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 315 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6881 (ptp90) REVERT: A 395 TRP cc_start: 0.5991 (OUTLIER) cc_final: 0.4819 (t-100) REVERT: A 410 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6460 (tm-30) REVERT: A 487 GLU cc_start: 0.7572 (mp0) cc_final: 0.7335 (pt0) REVERT: A 644 LYS cc_start: 0.7313 (pttm) cc_final: 0.6706 (pmtt) REVERT: A 1009 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: A 1022 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7153 (tp) REVERT: A 1033 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: A 1118 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7795 (mtm180) REVERT: A 1149 LYS cc_start: 0.7430 (ttmm) cc_final: 0.6747 (ptpt) REVERT: A 1164 ASP cc_start: 0.8381 (p0) cc_final: 0.8128 (p0) REVERT: A 1268 TYR cc_start: 0.8265 (m-10) cc_final: 0.7271 (m-10) REVERT: A 1408 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.5854 (m-10) REVERT: A 1421 ASN cc_start: 0.7101 (t0) cc_final: 0.6172 (t0) REVERT: A 1425 ASN cc_start: 0.6897 (m-40) cc_final: 0.6585 (m-40) REVERT: A 1467 LYS cc_start: 0.6442 (mmtp) cc_final: 0.5188 (ttpt) REVERT: A 1585 MET cc_start: 0.7569 (ttp) cc_final: 0.7314 (ttm) REVERT: A 1681 LYS cc_start: 0.7146 (tttt) cc_final: 0.6366 (ttmm) outliers start: 60 outliers final: 24 residues processed: 209 average time/residue: 0.5344 time to fit residues: 121.2420 Evaluate side-chains 192 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1680 HIS Chi-restraints excluded: chain A residue 1708 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS A1115 GLN A1354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114394 restraints weight = 13383.096| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.85 r_work: 0.3246 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11367 Z= 0.130 Angle : 0.524 8.509 15369 Z= 0.270 Chirality : 0.039 0.172 1721 Planarity : 0.004 0.049 1926 Dihedral : 5.949 77.325 1468 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.74 % Allowed : 26.02 % Favored : 69.24 % 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: 0.64 (0.23), residues: 1336 helix: 1.18 (0.18), residues: 751 sheet: -0.34 (0.61), residues: 77 loop : -0.50 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 825 TYR 0.018 0.001 TYR A 747 PHE 0.024 0.001 PHE A 418 TRP 0.017 0.001 TRP A 340 HIS 0.005 0.001 HIS A1626 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11366) covalent geometry : angle 0.52400 / 0.27 (15369) hydrogen bonds : bond 0.03882 / 2.56 ( 593) hydrogen bonds : angle 4.17809 / 3.00 ( 1746) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7742 (p0) REVERT: A 293 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 395 TRP cc_start: 0.5831 (OUTLIER) cc_final: 0.4695 (t-100) REVERT: A 410 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6323 (tm-30) REVERT: A 552 THR cc_start: 0.6810 (OUTLIER) cc_final: 0.6370 (p) REVERT: A 564 MET cc_start: 0.8497 (mmt) cc_final: 0.8282 (mpt) REVERT: A 644 LYS cc_start: 0.7263 (pttm) cc_final: 0.6706 (pmtt) REVERT: A 996 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7630 (p0) REVERT: A 1009 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7073 (mm-30) REVERT: A 1010 ILE cc_start: 0.7350 (mt) cc_final: 0.7102 (mt) REVERT: A 1022 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7260 (tp) REVERT: A 1149 LYS cc_start: 0.7388 (ttmm) cc_final: 0.6662 (ptpt) REVERT: A 1164 ASP cc_start: 0.8350 (p0) cc_final: 0.8075 (p0) REVERT: A 1268 TYR cc_start: 0.8272 (m-10) cc_final: 0.7228 (m-10) REVERT: A 1344 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7015 (tm) REVERT: A 1408 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.5800 (m-10) REVERT: A 1425 ASN cc_start: 0.6810 (m-40) cc_final: 0.6559 (m-40) REVERT: A 1467 LYS cc_start: 0.6319 (mmtp) cc_final: 0.5118 (ttpt) REVERT: A 1585 MET cc_start: 0.7489 (ttp) cc_final: 0.7139 (ttm) REVERT: A 1680 HIS cc_start: 0.6147 (OUTLIER) cc_final: 0.5793 (t-90) REVERT: A 1681 LYS cc_start: 0.7111 (tttt) cc_final: 0.6308 (ttmm) outliers start: 59 outliers final: 19 residues processed: 213 average time/residue: 0.5042 time to fit residues: 117.1589 Evaluate side-chains 187 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1680 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 122 optimal weight: 0.0470 chunk 116 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS A1415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115227 restraints weight = 13335.654| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.84 r_work: 0.3293 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11367 Z= 0.122 Angle : 0.504 7.826 15369 Z= 0.262 Chirality : 0.039 0.187 1721 Planarity : 0.003 0.047 1926 Dihedral : 5.711 77.772 1468 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.90 % Allowed : 26.75 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1336 helix: 1.43 (0.18), residues: 749 sheet: -0.54 (0.63), residues: 68 loop : -0.44 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 554 TYR 0.016 0.001 TYR A 670 PHE 0.011 0.001 PHE A 326 TRP 0.018 0.001 TRP A 340 HIS 0.004 0.001 HIS A1626 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11366) covalent geometry : angle 0.50421 / 0.26 (15369) hydrogen bonds : bond 0.03621 / 2.39 ( 593) hydrogen bonds : angle 4.02192 / 2.89 ( 1746) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7958 (pt0) REVERT: A 315 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6846 (ptp90) REVERT: A 395 TRP cc_start: 0.5763 (OUTLIER) cc_final: 0.4683 (t-100) REVERT: A 405 LEU cc_start: 0.5495 (OUTLIER) cc_final: 0.5245 (tt) REVERT: A 410 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6401 (tm-30) REVERT: A 552 THR cc_start: 0.6787 (OUTLIER) cc_final: 0.6387 (p) REVERT: A 644 LYS cc_start: 0.7319 (pttm) cc_final: 0.6747 (pmtt) REVERT: A 996 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 1010 ILE cc_start: 0.7386 (mt) cc_final: 0.7146 (mt) REVERT: A 1022 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7250 (tp) REVERT: A 1104 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 1118 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7494 (mtm180) REVERT: A 1138 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.6748 (mp) REVERT: A 1149 LYS cc_start: 0.7379 (ttmm) cc_final: 0.6651 (ptpt) REVERT: A 1164 ASP cc_start: 0.8252 (p0) cc_final: 0.7956 (p0) REVERT: A 1268 TYR cc_start: 0.8314 (m-10) cc_final: 0.7343 (m-10) REVERT: A 1344 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7175 (tm) REVERT: A 1408 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5740 (m-10) REVERT: A 1421 ASN cc_start: 0.7086 (t0) cc_final: 0.6160 (t0) REVERT: A 1425 ASN cc_start: 0.6840 (m-40) cc_final: 0.6606 (m-40) REVERT: A 1467 LYS cc_start: 0.6310 (mmtp) cc_final: 0.5090 (tttt) REVERT: A 1585 MET cc_start: 0.7510 (ttp) cc_final: 0.7175 (ttm) REVERT: A 1680 HIS cc_start: 0.6047 (OUTLIER) cc_final: 0.5786 (t-90) REVERT: A 1681 LYS cc_start: 0.7026 (tttt) cc_final: 0.6202 (ttmm) REVERT: A 1708 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7766 (m-30) outliers start: 61 outliers final: 22 residues processed: 217 average time/residue: 0.5052 time to fit residues: 119.3784 Evaluate side-chains 200 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1680 HIS Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1713 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 73 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS A1115 GLN A1290 GLN A1415 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116803 restraints weight = 13181.174| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.98 r_work: 0.3245 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11367 Z= 0.144 Angle : 0.525 8.878 15369 Z= 0.270 Chirality : 0.040 0.188 1721 Planarity : 0.003 0.047 1926 Dihedral : 5.541 77.395 1466 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.82 % Allowed : 26.91 % Favored : 68.27 % 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: 0.93 (0.23), residues: 1336 helix: 1.48 (0.18), residues: 750 sheet: -0.59 (0.62), residues: 68 loop : -0.44 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 554 TYR 0.020 0.001 TYR A 670 PHE 0.026 0.001 PHE A 418 TRP 0.021 0.001 TRP A 340 HIS 0.005 0.001 HIS A1626 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (11366) covalent geometry : angle 0.52541 / 0.27 (15369) hydrogen bonds : bond 0.03711 / 2.44 ( 593) hydrogen bonds : angle 4.01531 / 2.88 ( 1746) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7776 (p0) REVERT: A 293 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: A 315 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6860 (ptp90) REVERT: A 395 TRP cc_start: 0.5925 (OUTLIER) cc_final: 0.4848 (t-100) REVERT: A 410 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6393 (tm-30) REVERT: A 552 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6412 (p) REVERT: A 564 MET cc_start: 0.8628 (mmt) cc_final: 0.8428 (mpt) REVERT: A 644 LYS cc_start: 0.7432 (pttm) cc_final: 0.6861 (pmtt) REVERT: A 996 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 1118 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7514 (mtm180) REVERT: A 1138 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.6892 (mp) REVERT: A 1149 LYS cc_start: 0.7527 (ttmm) cc_final: 0.6769 (pttp) REVERT: A 1164 ASP cc_start: 0.8373 (p0) cc_final: 0.8076 (p0) REVERT: A 1268 TYR cc_start: 0.8436 (m-10) cc_final: 0.7453 (m-10) REVERT: A 1344 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7203 (tm) REVERT: A 1408 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5836 (m-10) REVERT: A 1425 ASN cc_start: 0.6899 (m-40) cc_final: 0.6651 (m-40) REVERT: A 1467 LYS cc_start: 0.6379 (mmtp) cc_final: 0.5105 (tttt) REVERT: A 1585 MET cc_start: 0.7587 (ttp) cc_final: 0.7246 (ttm) REVERT: A 1680 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.5873 (t-90) REVERT: A 1681 LYS cc_start: 0.7188 (tttt) cc_final: 0.6321 (ttmm) REVERT: A 1708 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7874 (m-30) outliers start: 60 outliers final: 25 residues processed: 215 average time/residue: 0.5211 time to fit residues: 121.6268 Evaluate side-chains 198 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1522 VAL Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1680 HIS Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1713 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS A1115 GLN A1415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116473 restraints weight = 13191.482| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.84 r_work: 0.3238 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11367 Z= 0.130 Angle : 0.517 9.746 15369 Z= 0.265 Chirality : 0.040 0.211 1721 Planarity : 0.003 0.046 1926 Dihedral : 5.408 77.779 1463 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.82 % Allowed : 27.47 % Favored : 67.71 % 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: 1.01 (0.23), residues: 1336 helix: 1.55 (0.18), residues: 751 sheet: -0.50 (0.62), residues: 68 loop : -0.41 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 554 TYR 0.018 0.001 TYR A 747 PHE 0.027 0.001 PHE A 418 TRP 0.022 0.001 TRP A 340 HIS 0.006 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11366) covalent geometry : angle 0.51656 / 0.26 (15369) hydrogen bonds : bond 0.03608 / 2.37 ( 593) hydrogen bonds : angle 3.95328 / 2.84 ( 1746) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7718 (p0) REVERT: A 293 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: A 300 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8139 (mtmm) REVERT: A 315 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6795 (ptp90) REVERT: A 395 TRP cc_start: 0.5819 (OUTLIER) cc_final: 0.4754 (t60) REVERT: A 410 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6391 (tm-30) REVERT: A 552 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6376 (p) REVERT: A 564 MET cc_start: 0.8531 (mmt) cc_final: 0.8322 (mpt) REVERT: A 572 MET cc_start: 0.7836 (tmm) cc_final: 0.7517 (tmt) REVERT: A 644 LYS cc_start: 0.7385 (pttm) cc_final: 0.6786 (pmtt) REVERT: A 764 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5807 (ttt) REVERT: A 996 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7517 (p0) REVERT: A 1022 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7229 (tp) REVERT: A 1118 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: A 1149 LYS cc_start: 0.7407 (ttmm) cc_final: 0.6642 (pttp) REVERT: A 1164 ASP cc_start: 0.8376 (p0) cc_final: 0.8063 (p0) REVERT: A 1182 ILE cc_start: 0.8439 (mm) cc_final: 0.8211 (mm) REVERT: A 1268 TYR cc_start: 0.8388 (m-10) cc_final: 0.7413 (m-10) REVERT: A 1344 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7385 (pp) REVERT: A 1408 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5800 (m-10) REVERT: A 1467 LYS cc_start: 0.6264 (mmtp) cc_final: 0.5056 (tttt) REVERT: A 1585 MET cc_start: 0.7553 (ttp) cc_final: 0.7201 (ttm) REVERT: A 1680 HIS cc_start: 0.5996 (OUTLIER) cc_final: 0.5777 (t-90) REVERT: A 1681 LYS cc_start: 0.7212 (tttt) cc_final: 0.6365 (ttmm) REVERT: A 1708 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7848 (m-30) outliers start: 60 outliers final: 29 residues processed: 208 average time/residue: 0.5025 time to fit residues: 114.2847 Evaluate side-chains 208 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1680 HIS Chi-restraints excluded: chain A residue 1694 SER Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1713 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 80 optimal weight: 0.0170 chunk 11 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS A1115 GLN A1415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120023 restraints weight = 13122.289| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.84 r_work: 0.3244 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11367 Z= 0.117 Angle : 0.521 9.162 15369 Z= 0.265 Chirality : 0.039 0.201 1721 Planarity : 0.003 0.045 1926 Dihedral : 5.364 77.995 1463 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.98 % Allowed : 28.11 % Favored : 66.91 % 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: 1.10 (0.23), residues: 1336 helix: 1.64 (0.18), residues: 751 sheet: -0.33 (0.63), residues: 68 loop : -0.42 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 554 TYR 0.017 0.001 TYR A 747 PHE 0.010 0.001 PHE A 326 TRP 0.028 0.001 TRP A 340 HIS 0.008 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11366) covalent geometry : angle 0.52118 / 0.26 (15369) hydrogen bonds : bond 0.03500 / 2.30 ( 593) hydrogen bonds : angle 3.89193 / 2.80 ( 1746) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7717 (p0) REVERT: A 293 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: A 300 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8119 (mtmm) REVERT: A 315 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6685 (ptp90) REVERT: A 395 TRP cc_start: 0.5778 (OUTLIER) cc_final: 0.4692 (t60) REVERT: A 410 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6324 (tm-30) REVERT: A 552 THR cc_start: 0.6744 (OUTLIER) cc_final: 0.6354 (p) REVERT: A 572 MET cc_start: 0.7961 (tmm) cc_final: 0.7723 (tmt) REVERT: A 644 LYS cc_start: 0.7341 (pttm) cc_final: 0.6711 (pmtt) REVERT: A 764 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5848 (ttt) REVERT: A 906 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: A 1022 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7228 (tp) REVERT: A 1118 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7476 (mtm180) REVERT: A 1149 LYS cc_start: 0.7367 (ttmm) cc_final: 0.6579 (pttp) REVERT: A 1164 ASP cc_start: 0.8269 (p0) cc_final: 0.7952 (p0) REVERT: A 1268 TYR cc_start: 0.8366 (m-10) cc_final: 0.7510 (m-10) REVERT: A 1344 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7376 (pp) REVERT: A 1408 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5835 (m-10) REVERT: A 1467 LYS cc_start: 0.6192 (mmtp) cc_final: 0.4992 (tttt) REVERT: A 1585 MET cc_start: 0.7517 (ttp) cc_final: 0.7210 (ttm) REVERT: A 1681 LYS cc_start: 0.7200 (tttt) cc_final: 0.6364 (ttmm) REVERT: A 1708 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7823 (m-30) outliers start: 62 outliers final: 31 residues processed: 218 average time/residue: 0.5389 time to fit residues: 127.9419 Evaluate side-chains 210 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1028 HIS Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1694 SER Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1713 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS A1115 GLN A1415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116810 restraints weight = 13125.949| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.84 r_work: 0.3258 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11367 Z= 0.153 Angle : 0.542 8.082 15369 Z= 0.277 Chirality : 0.040 0.199 1721 Planarity : 0.003 0.046 1926 Dihedral : 5.379 77.090 1463 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.02 % Allowed : 29.08 % Favored : 66.91 % 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: 1.02 (0.23), residues: 1336 helix: 1.56 (0.18), residues: 752 sheet: -0.40 (0.62), residues: 68 loop : -0.44 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 554 TYR 0.019 0.001 TYR A 670 PHE 0.028 0.001 PHE A 418 TRP 0.034 0.002 TRP A 340 HIS 0.015 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (11366) covalent geometry : angle 0.54232 / 0.28 (15369) hydrogen bonds : bond 0.03663 / 2.41 ( 593) hydrogen bonds : angle 3.95903 / 2.85 ( 1746) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7689 (p0) REVERT: A 293 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 300 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8138 (mtmm) REVERT: A 315 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6815 (ptp90) REVERT: A 395 TRP cc_start: 0.5897 (OUTLIER) cc_final: 0.4800 (t60) REVERT: A 410 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6359 (tm-30) REVERT: A 552 THR cc_start: 0.6804 (OUTLIER) cc_final: 0.6412 (p) REVERT: A 564 MET cc_start: 0.8554 (mmt) cc_final: 0.8352 (mpt) REVERT: A 644 LYS cc_start: 0.7395 (pttm) cc_final: 0.6745 (pmtt) REVERT: A 764 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5911 (ttt) REVERT: A 906 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: A 1118 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7638 (mtm180) REVERT: A 1149 LYS cc_start: 0.7409 (ttmm) cc_final: 0.6651 (pttp) REVERT: A 1164 ASP cc_start: 0.8400 (p0) cc_final: 0.8096 (p0) REVERT: A 1268 TYR cc_start: 0.8420 (m-10) cc_final: 0.7448 (m-10) REVERT: A 1344 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7420 (pp) REVERT: A 1408 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.5853 (m-10) REVERT: A 1421 ASN cc_start: 0.6938 (t0) cc_final: 0.6470 (t0) REVERT: A 1467 LYS cc_start: 0.6243 (mmtp) cc_final: 0.5055 (ttpt) REVERT: A 1480 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7121 (tt0) REVERT: A 1585 MET cc_start: 0.7602 (ttp) cc_final: 0.7314 (ttm) REVERT: A 1681 LYS cc_start: 0.7177 (tttt) cc_final: 0.6386 (ttmm) REVERT: A 1696 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: A 1708 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7818 (m-30) outliers start: 50 outliers final: 31 residues processed: 203 average time/residue: 0.5240 time to fit residues: 115.9500 Evaluate side-chains 207 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1694 SER Chi-restraints excluded: chain A residue 1696 GLU Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1713 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS A1115 GLN A1154 ASN A1415 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115769 restraints weight = 13190.058| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.82 r_work: 0.3257 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11367 Z= 0.129 Angle : 0.545 10.810 15369 Z= 0.275 Chirality : 0.040 0.193 1721 Planarity : 0.003 0.045 1926 Dihedral : 5.368 77.317 1463 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.10 % Allowed : 29.16 % Favored : 66.75 % 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: 1336 helix: 1.62 (0.18), residues: 752 sheet: -0.32 (0.62), residues: 68 loop : -0.44 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 554 TYR 0.017 0.001 TYR A 670 PHE 0.010 0.001 PHE A 683 TRP 0.042 0.001 TRP A 340 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11366) covalent geometry : angle 0.54511 / 0.27 (15369) hydrogen bonds : bond 0.03563 / 2.34 ( 593) hydrogen bonds : angle 3.93457 / 2.83 ( 1746) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7738 (p0) REVERT: A 293 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 300 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8086 (mtmm) REVERT: A 315 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.6767 (ptp90) REVERT: A 395 TRP cc_start: 0.5873 (OUTLIER) cc_final: 0.4787 (t60) REVERT: A 410 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6292 (tm-30) REVERT: A 552 THR cc_start: 0.6815 (OUTLIER) cc_final: 0.6414 (p) REVERT: A 644 LYS cc_start: 0.7395 (pttm) cc_final: 0.6734 (pmtt) REVERT: A 764 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5815 (ttt) REVERT: A 906 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: A 1118 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7500 (mtm180) REVERT: A 1149 LYS cc_start: 0.7397 (ttmm) cc_final: 0.6633 (pttp) REVERT: A 1164 ASP cc_start: 0.8393 (p0) cc_final: 0.8074 (p0) REVERT: A 1268 TYR cc_start: 0.8407 (m-10) cc_final: 0.7571 (m-10) REVERT: A 1290 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7219 (mt0) REVERT: A 1344 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7372 (pp) REVERT: A 1408 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5842 (m-10) REVERT: A 1467 LYS cc_start: 0.6215 (mmtp) cc_final: 0.5037 (tttt) REVERT: A 1681 LYS cc_start: 0.7173 (tttt) cc_final: 0.6373 (ttmm) REVERT: A 1696 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6154 (mp0) REVERT: A 1708 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7804 (m-30) outliers start: 51 outliers final: 31 residues processed: 200 average time/residue: 0.5250 time to fit residues: 114.1059 Evaluate side-chains 207 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1522 VAL Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1694 SER Chi-restraints excluded: chain A residue 1696 GLU Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1713 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 78 optimal weight: 0.0970 chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 92 optimal weight: 0.0470 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 826 ASN A1028 HIS A1115 GLN A1154 ASN A1415 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119046 restraints weight = 13182.803| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.83 r_work: 0.3289 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11367 Z= 0.103 Angle : 0.512 7.960 15369 Z= 0.265 Chirality : 0.038 0.167 1721 Planarity : 0.003 0.040 1926 Dihedral : 5.308 78.326 1463 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.05 % Allowed : 30.20 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1336 helix: 1.80 (0.18), residues: 752 sheet: -0.17 (0.63), residues: 68 loop : -0.41 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 235 TYR 0.016 0.001 TYR A 747 PHE 0.024 0.001 PHE A 418 TRP 0.040 0.001 TRP A 340 HIS 0.004 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (11366) covalent geometry : angle 0.51220 / 0.26 (15369) hydrogen bonds : bond 0.03289 / 2.17 ( 593) hydrogen bonds : angle 3.80157 / 2.73 ( 1746) Misc. bond : bond 0.00009 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7600 (p0) REVERT: A 293 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: A 300 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8074 (mtmm) REVERT: A 315 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6666 (ptp90) REVERT: A 410 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6238 (tm-30) REVERT: A 452 MET cc_start: 0.7983 (tpt) cc_final: 0.7251 (pp-130) REVERT: A 552 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6277 (p) REVERT: A 588 PHE cc_start: 0.8071 (m-80) cc_final: 0.7710 (m-80) REVERT: A 644 LYS cc_start: 0.7364 (pttm) cc_final: 0.6712 (pmtt) REVERT: A 730 SER cc_start: 0.8703 (t) cc_final: 0.8494 (t) REVERT: A 764 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5885 (ttt) REVERT: A 906 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: A 1118 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7525 (mtm180) REVERT: A 1149 LYS cc_start: 0.7321 (ttmm) cc_final: 0.6599 (ptpt) REVERT: A 1164 ASP cc_start: 0.8148 (p0) cc_final: 0.7829 (p0) REVERT: A 1268 TYR cc_start: 0.8264 (m-10) cc_final: 0.7446 (m-10) REVERT: A 1290 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: A 1344 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7179 (tm) REVERT: A 1408 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5684 (m-10) REVERT: A 1421 ASN cc_start: 0.6816 (t0) cc_final: 0.6394 (t0) REVERT: A 1467 LYS cc_start: 0.6187 (mmtp) cc_final: 0.5007 (tttt) REVERT: A 1480 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7010 (tt0) REVERT: A 1575 GLN cc_start: 0.7749 (mt0) cc_final: 0.7482 (mt0) REVERT: A 1681 LYS cc_start: 0.7167 (tttt) cc_final: 0.6363 (ttmm) REVERT: A 1696 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6151 (mp0) outliers start: 38 outliers final: 19 residues processed: 207 average time/residue: 0.5574 time to fit residues: 124.9547 Evaluate side-chains 200 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1118 ARG Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1696 GLU Chi-restraints excluded: chain A residue 1713 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1028 HIS ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 GLN A1415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120182 restraints weight = 13129.539| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.98 r_work: 0.3258 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11367 Z= 0.129 Angle : 0.546 9.659 15369 Z= 0.276 Chirality : 0.040 0.177 1721 Planarity : 0.003 0.041 1926 Dihedral : 5.307 76.819 1463 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.29 % Allowed : 30.28 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.25 (0.23), residues: 1336 helix: 1.80 (0.18), residues: 752 sheet: -0.23 (0.62), residues: 68 loop : -0.44 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 825 TYR 0.016 0.001 TYR A 670 PHE 0.009 0.001 PHE A 683 TRP 0.049 0.002 TRP A 340 HIS 0.007 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11366) covalent geometry : angle 0.54561 / 0.28 (15369) hydrogen bonds : bond 0.03481 / 2.29 ( 593) hydrogen bonds : angle 3.85577 / 2.77 ( 1746) Misc. bond : bond 0.00054 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3862.05 seconds wall clock time: 66 minutes 47.38 seconds (4007.38 seconds total)