Starting phenix.real_space_refine on Wed Mar 4 01:04:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eei_31077/03_2026/7eei_31077.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eei_31077/03_2026/7eei_31077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2026/7eei_31077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2026/7eei_31077.map" model { file = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2026/7eei_31077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eei_31077/03_2026/7eei_31077.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 65 5.16 5 C 6290 2.51 5 N 1723 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A ASP 337": not complete - not flipped Residue "A ASP 444": not complete - not flipped Residue "A ASP 640": not complete - not flipped Residue "A GLU 702": not complete - not flipped Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9825 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 9825 Classifications: {'peptide': 1400} Incomplete info: {'backbone_only': 48, 'n_c_alpha_c_only': 14, 'truncation_to_alanine': 250} Link IDs: {'PTRANS': 58, 'TRANS': 1341} Unresolved chain links: 1 Unresolved chain link angles: 29 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1425 Unresolved non-hydrogen angles: 1855 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLU:plan': 64, 'ARG:plan': 29, 'ASN:plan1': 19, 'ASP:plan': 46, 'GLN:plan1': 18, 'TRP:plan': 4, 'PHE:plan': 14, 'TYR:plan': 8, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 799 Time building chain proxies: 2.38, per 1000 atoms: 0.24 Number of scatterers: 9825 At special positions: 0 Unit cell: (87.48, 112.32, 95.04, 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 65 16.00 O 1747 8.00 N 1723 7.00 C 6290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 986 " - pdb=" SG CYS A1159 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 554.7 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 53.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.794A pdb=" N THR A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.505A pdb=" N PHE A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 280 removed outlier: 3.674A pdb=" N ILE A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 311 removed outlier: 3.757A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.952A pdb=" N ALA A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.678A pdb=" N GLN A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 457 removed outlier: 3.791A pdb=" N CYS A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.647A pdb=" N LEU A 472 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 507 through 530 removed outlier: 4.629A pdb=" N TRP A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.682A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 640 through 659 Processing helix chain 'A' and resid 661 through 677 removed outlier: 3.527A pdb=" N GLU A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.501A pdb=" N SER A 693 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 695 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 721 Processing helix chain 'A' and resid 748 through 756 removed outlier: 3.682A pdb=" N LEU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 removed outlier: 4.081A pdb=" N LYS A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 781 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 785 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 Processing helix chain 'A' and resid 830 through 846 removed outlier: 3.692A pdb=" N ILE A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 removed outlier: 3.569A pdb=" N LEU A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 894 through 910 removed outlier: 4.736A pdb=" N ASP A 901 " --> pdb=" O GLN A 897 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 952 Processing helix chain 'A' and resid 960 through 979 removed outlier: 3.700A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Proline residue: A 968 - end of helix removed outlier: 4.540A pdb=" N GLY A 972 " --> pdb=" O PRO A 968 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1012 removed outlier: 3.573A pdb=" N PHE A1011 " --> pdb=" O MET A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1015 No H-bonds generated for 'chain 'A' and resid 1013 through 1015' Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 4.088A pdb=" N ARG A1029 " --> pdb=" O SER A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1044 removed outlier: 3.825A pdb=" N GLY A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1089 through 1116 removed outlier: 3.793A pdb=" N SER A1106 " --> pdb=" O GLU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1121 removed outlier: 4.239A pdb=" N SER A1121 " --> pdb=" O PRO A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1164 removed outlier: 3.805A pdb=" N LYS A1163 " --> pdb=" O CYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1207 Processing helix chain 'A' and resid 1219 through 1235 Processing helix chain 'A' and resid 1238 through 1257 Processing helix chain 'A' and resid 1263 through 1275 removed outlier: 3.829A pdb=" N GLU A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1271 " --> pdb=" O GLU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'A' and resid 1295 through 1307 Processing helix chain 'A' and resid 1308 through 1316 Processing helix chain 'A' and resid 1358 through 1368 Processing helix chain 'A' and resid 1374 through 1380 removed outlier: 4.159A pdb=" N ILE A1378 " --> pdb=" O TRP A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1384 Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1409 through 1414 Processing helix chain 'A' and resid 1416 through 1427 removed outlier: 3.520A pdb=" N LYS A1420 " --> pdb=" O ASN A1416 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A1425 " --> pdb=" O VAL A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1457 Processing helix chain 'A' and resid 1459 through 1469 removed outlier: 4.531A pdb=" N GLU A1469 " --> pdb=" O PHE A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1496 removed outlier: 3.607A pdb=" N ILE A1496 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1510 Processing helix chain 'A' and resid 1518 through 1530 Proline residue: A1525 - end of helix removed outlier: 3.888A pdb=" N LEU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1559 Processing helix chain 'A' and resid 1574 through 1582 Processing helix chain 'A' and resid 1976 through 1989 removed outlier: 4.110A pdb=" N SER A1980 " --> pdb=" O ASN A1976 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.230A pdb=" N ALA A 416 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 537 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.230A pdb=" N ALA A 416 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 537 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 724 through 727 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 857 Processing sheet with id=AA5, first strand: chain 'A' and resid 928 through 931 removed outlier: 7.293A pdb=" N ILE A 914 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id=AA7, first strand: chain 'A' and resid 1490 through 1491 509 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 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: 1.21 - 1.34: 3136 1.34 - 1.47: 2541 1.47 - 1.60: 4265 1.60 - 1.73: 1 1.73 - 1.86: 95 Bond restraints: 10038 Sorted by residual: bond pdb=" CB PHE A 495 " pdb=" CG PHE A 495 " ideal model delta sigma weight residual 1.502 1.600 -0.098 2.30e-02 1.89e+03 1.80e+01 bond pdb=" N GLU A1165 " pdb=" CA GLU A1165 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.15e-02 7.56e+03 1.50e+01 bond pdb=" CA PHE A 495 " pdb=" CB PHE A 495 " ideal model delta sigma weight residual 1.527 1.571 -0.044 1.44e-02 4.82e+03 9.32e+00 bond pdb=" N VAL A1421 " pdb=" CA VAL A1421 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.16e+00 bond pdb=" C GLY A 494 " pdb=" N PHE A 495 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.26e-02 6.30e+03 8.76e+00 ... (remaining 10033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 13076 2.52 - 5.04: 441 5.04 - 7.57: 62 7.57 - 10.09: 12 10.09 - 12.61: 3 Bond angle restraints: 13594 Sorted by residual: angle pdb=" N PHE A 495 " pdb=" CA PHE A 495 " pdb=" C PHE A 495 " ideal model delta sigma weight residual 110.19 101.16 9.03 1.24e+00 6.50e-01 5.31e+01 angle pdb=" CA PHE A 495 " pdb=" C PHE A 495 " pdb=" N ASN A 496 " ideal model delta sigma weight residual 115.58 126.50 -10.92 1.55e+00 4.16e-01 4.96e+01 angle pdb=" CA PHE A 495 " pdb=" C PHE A 495 " pdb=" O PHE A 495 " ideal model delta sigma weight residual 122.01 116.20 5.81 1.05e+00 9.07e-01 3.06e+01 angle pdb=" N SER A 323 " pdb=" CA SER A 323 " pdb=" C SER A 323 " ideal model delta sigma weight residual 110.35 118.09 -7.74 1.40e+00 5.10e-01 3.06e+01 angle pdb=" C SER A 322 " pdb=" N SER A 323 " pdb=" CA SER A 323 " ideal model delta sigma weight residual 121.31 129.15 -7.84 1.49e+00 4.50e-01 2.77e+01 ... (remaining 13589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.67: 5620 22.67 - 45.35: 240 45.35 - 68.02: 43 68.02 - 90.70: 7 90.70 - 113.37: 2 Dihedral angle restraints: 5912 sinusoidal: 1949 harmonic: 3963 Sorted by residual: dihedral pdb=" CA ASP A 574 " pdb=" C ASP A 574 " pdb=" N LEU A 575 " pdb=" CA LEU A 575 " ideal model delta harmonic sigma weight residual 180.00 123.42 56.58 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA SER A 322 " pdb=" C SER A 322 " pdb=" N SER A 323 " pdb=" CA SER A 323 " ideal model delta harmonic sigma weight residual -180.00 -126.77 -53.23 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CB CYS A 986 " pdb=" SG CYS A 986 " pdb=" SG CYS A1159 " pdb=" CB CYS A1159 " ideal model delta sinusoidal sigma weight residual -86.00 -160.07 74.07 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1203 0.065 - 0.129: 265 0.129 - 0.194: 48 0.194 - 0.259: 6 0.259 - 0.323: 3 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CB ILE A 781 " pdb=" CA ILE A 781 " pdb=" CG1 ILE A 781 " pdb=" CG2 ILE A 781 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PHE A 495 " pdb=" N PHE A 495 " pdb=" C PHE A 495 " pdb=" CB PHE A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1522 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 573 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C PHE A 573 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE A 573 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 574 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1563 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A1564 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1564 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1564 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 495 " -0.015 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C PHE A 495 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE A 495 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 496 " -0.017 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 46 2.56 - 3.15: 8266 3.15 - 3.73: 15368 3.73 - 4.32: 20314 4.32 - 4.90: 33823 Nonbonded interactions: 77817 Sorted by model distance: nonbonded pdb=" O ASN A 960 " pdb=" OD1 ASN A 960 " model vdw 1.975 3.040 nonbonded pdb=" NE2 GLN A 483 " pdb=" CD1 PHE A 495 " model vdw 1.992 3.420 nonbonded pdb=" NE2 GLN A 483 " pdb=" CE1 PHE A 495 " model vdw 2.169 3.420 nonbonded pdb=" O ALA A 792 " pdb=" N LYS A 797 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS A 339 " pdb=" O VAL A1261 " model vdw 2.237 3.120 ... (remaining 77812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.210 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.006 0.098 10039 Z= 0.323 Angle : 1.091 12.610 13596 Z= 0.627 Chirality : 0.057 0.323 1525 Planarity : 0.007 0.070 1748 Dihedral : 13.713 113.372 3377 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.22 % 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: -1.90 (0.20), residues: 1396 helix: -0.33 (0.19), residues: 653 sheet: -2.60 (0.53), residues: 65 loop : -2.08 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 316 TYR 0.020 0.003 TYR A1169 PHE 0.045 0.003 PHE A 495 TRP 0.015 0.002 TRP A1275 HIS 0.011 0.002 HIS A 913 Details of bonding type rmsd covalent geometry : bond 0.00631 (10038) covalent geometry : angle 1.08993 (13594) SS BOND : bond 0.01244 ( 1) SS BOND : angle 3.31163 ( 2) hydrogen bonds : bond 0.15527 ( 497) hydrogen bonds : angle 6.93101 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 602 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 248 ASP cc_start: 0.8281 (m-30) cc_final: 0.8063 (m-30) REVERT: A 700 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7403 (mmm160) REVERT: A 727 LYS cc_start: 0.5501 (tttt) cc_final: 0.5108 (mttt) REVERT: A 757 TYR cc_start: 0.8378 (m-80) cc_final: 0.7943 (m-80) REVERT: A 1059 PHE cc_start: 0.8636 (t80) cc_final: 0.8432 (t80) REVERT: A 1107 LEU cc_start: 0.9126 (tp) cc_final: 0.8899 (tt) REVERT: A 1187 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 1580 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6657 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.0921 time to fit residues: 33.5098 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 439 GLN A 785 HIS A1100 HIS A1197 GLN A1276 ASN A1287 ASN A1381 ASN A1479 ASN A1570 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092628 restraints weight = 20363.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095500 restraints weight = 10190.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097404 restraints weight = 6550.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098599 restraints weight = 4932.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099184 restraints weight = 4152.295| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10039 Z= 0.199 Angle : 0.662 8.207 13596 Z= 0.349 Chirality : 0.045 0.150 1525 Planarity : 0.005 0.061 1748 Dihedral : 5.181 37.283 1473 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.27 % Allowed : 13.82 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.91 (0.22), residues: 1396 helix: 0.68 (0.19), residues: 676 sheet: -2.03 (0.56), residues: 67 loop : -1.88 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1029 TYR 0.013 0.002 TYR A1091 PHE 0.016 0.002 PHE A 247 TRP 0.016 0.002 TRP A1328 HIS 0.019 0.002 HIS A1063 Details of bonding type rmsd covalent geometry : bond 0.00447 (10038) covalent geometry : angle 0.66104 (13594) SS BOND : bond 0.00411 ( 1) SS BOND : angle 2.87600 ( 2) hydrogen bonds : bond 0.04983 ( 497) hydrogen bonds : angle 4.83991 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.268 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 258 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 262 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8524 (ttp-170) REVERT: A 727 LYS cc_start: 0.6047 (tttt) cc_final: 0.5655 (mtpt) REVERT: A 850 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8367 (mmm-85) REVERT: A 929 TYR cc_start: 0.8241 (m-80) cc_final: 0.7922 (m-80) REVERT: A 1578 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8707 (tp40) outliers start: 27 outliers final: 14 residues processed: 193 average time/residue: 0.0744 time to fit residues: 21.7195 Evaluate side-chains 178 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1578 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS A1247 GLN ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095317 restraints weight = 20106.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098177 restraints weight = 10281.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100066 restraints weight = 6656.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101239 restraints weight = 5043.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101721 restraints weight = 4240.421| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10039 Z= 0.124 Angle : 0.577 7.652 13596 Z= 0.303 Chirality : 0.041 0.140 1525 Planarity : 0.005 0.055 1748 Dihedral : 4.841 41.316 1473 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.79 % Allowed : 15.27 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.45 (0.22), residues: 1396 helix: 1.12 (0.20), residues: 669 sheet: -1.22 (0.63), residues: 65 loop : -1.77 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1029 TYR 0.015 0.001 TYR A 867 PHE 0.016 0.001 PHE A1059 TRP 0.019 0.001 TRP A1559 HIS 0.011 0.001 HIS A1063 Details of bonding type rmsd covalent geometry : bond 0.00272 (10038) covalent geometry : angle 0.57630 (13594) SS BOND : bond 0.00445 ( 1) SS BOND : angle 2.03258 ( 2) hydrogen bonds : bond 0.04256 ( 497) hydrogen bonds : angle 4.51932 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.242 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 258 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 727 LYS cc_start: 0.5946 (tttt) cc_final: 0.5555 (mtpt) REVERT: A 850 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8312 (mmm-85) REVERT: A 929 TYR cc_start: 0.8167 (m-80) cc_final: 0.7905 (m-80) REVERT: A 1578 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8501 (tp40) outliers start: 23 outliers final: 16 residues processed: 193 average time/residue: 0.0743 time to fit residues: 21.7426 Evaluate side-chains 180 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Chi-restraints excluded: chain A residue 1578 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 134 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094105 restraints weight = 20280.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097062 restraints weight = 10052.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099009 restraints weight = 6384.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100234 restraints weight = 4769.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100595 restraints weight = 3979.853| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10039 Z= 0.137 Angle : 0.557 7.212 13596 Z= 0.294 Chirality : 0.041 0.139 1525 Planarity : 0.005 0.058 1748 Dihedral : 4.608 39.617 1473 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.00 % Allowed : 16.85 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.23), residues: 1396 helix: 1.32 (0.20), residues: 672 sheet: -0.68 (0.64), residues: 67 loop : -1.73 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1029 TYR 0.016 0.001 TYR A 867 PHE 0.015 0.001 PHE A 952 TRP 0.024 0.001 TRP A1559 HIS 0.006 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00308 (10038) covalent geometry : angle 0.55688 (13594) SS BOND : bond 0.00518 ( 1) SS BOND : angle 2.13035 ( 2) hydrogen bonds : bond 0.04171 ( 497) hydrogen bonds : angle 4.28029 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.366 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 727 LYS cc_start: 0.6018 (tttt) cc_final: 0.5626 (mtpt) REVERT: A 929 TYR cc_start: 0.8259 (m-80) cc_final: 0.7984 (m-80) REVERT: A 1307 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 1578 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8591 (tp40) outliers start: 33 outliers final: 23 residues processed: 192 average time/residue: 0.0704 time to fit residues: 20.7135 Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Chi-restraints excluded: chain A residue 1578 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092934 restraints weight = 20299.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095895 restraints weight = 10109.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097853 restraints weight = 6452.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098681 restraints weight = 4839.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099697 restraints weight = 4171.244| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10039 Z= 0.151 Angle : 0.563 7.104 13596 Z= 0.296 Chirality : 0.041 0.141 1525 Planarity : 0.005 0.060 1748 Dihedral : 4.604 39.442 1473 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.36 % Allowed : 17.58 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1396 helix: 1.40 (0.20), residues: 673 sheet: -0.50 (0.65), residues: 67 loop : -1.70 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 850 TYR 0.017 0.001 TYR A 584 PHE 0.014 0.001 PHE A1054 TRP 0.024 0.001 TRP A1559 HIS 0.007 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00343 (10038) covalent geometry : angle 0.56278 (13594) SS BOND : bond 0.00555 ( 1) SS BOND : angle 2.26632 ( 2) hydrogen bonds : bond 0.04198 ( 497) hydrogen bonds : angle 4.26236 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.265 Fit side-chains TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 727 LYS cc_start: 0.6099 (tttt) cc_final: 0.5682 (mtpt) REVERT: A 929 TYR cc_start: 0.8259 (m-80) cc_final: 0.7910 (m-10) REVERT: A 1078 LEU cc_start: 0.9200 (mp) cc_final: 0.8998 (mp) REVERT: A 1307 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7934 (p) REVERT: A 1568 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6971 (mp) REVERT: A 1578 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8659 (tp40) outliers start: 36 outliers final: 25 residues processed: 189 average time/residue: 0.0738 time to fit residues: 21.5670 Evaluate side-chains 189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1578 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1090 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094927 restraints weight = 20622.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097916 restraints weight = 10241.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099822 restraints weight = 6541.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101079 restraints weight = 4944.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101573 restraints weight = 4131.727| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10039 Z= 0.116 Angle : 0.552 9.308 13596 Z= 0.285 Chirality : 0.041 0.147 1525 Planarity : 0.005 0.062 1748 Dihedral : 4.363 35.859 1473 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.88 % Allowed : 18.67 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.00 (0.23), residues: 1396 helix: 1.53 (0.20), residues: 670 sheet: -0.36 (0.65), residues: 67 loop : -1.67 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 850 TYR 0.018 0.001 TYR A 867 PHE 0.019 0.001 PHE A1054 TRP 0.021 0.001 TRP A1559 HIS 0.007 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00263 (10038) covalent geometry : angle 0.55140 (13594) SS BOND : bond 0.00462 ( 1) SS BOND : angle 1.85625 ( 2) hydrogen bonds : bond 0.03835 ( 497) hydrogen bonds : angle 4.14240 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.394 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 462 TRP cc_start: 0.8093 (m100) cc_final: 0.7728 (m100) REVERT: A 568 ARG cc_start: 0.8160 (tpt90) cc_final: 0.7841 (tpt90) REVERT: A 659 GLU cc_start: 0.7912 (tt0) cc_final: 0.7702 (tt0) REVERT: A 727 LYS cc_start: 0.6289 (tttt) cc_final: 0.5881 (mtpt) REVERT: A 929 TYR cc_start: 0.8131 (m-80) cc_final: 0.7778 (m-10) REVERT: A 1307 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 1578 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8522 (tp40) REVERT: A 1580 ARG cc_start: 0.7129 (tpt170) cc_final: 0.6645 (tpm170) outliers start: 32 outliers final: 22 residues processed: 190 average time/residue: 0.0754 time to fit residues: 22.2048 Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Chi-restraints excluded: chain A residue 1578 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 16 optimal weight: 0.0070 chunk 33 optimal weight: 6.9990 chunk 137 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097679 restraints weight = 20211.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100702 restraints weight = 10009.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102701 restraints weight = 6345.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103796 restraints weight = 4730.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104729 restraints weight = 3990.166| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10039 Z= 0.104 Angle : 0.539 9.058 13596 Z= 0.277 Chirality : 0.040 0.143 1525 Planarity : 0.005 0.065 1748 Dihedral : 4.150 31.753 1473 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.48 % Allowed : 18.30 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.06 (0.23), residues: 1396 helix: 1.61 (0.20), residues: 675 sheet: -0.27 (0.71), residues: 65 loop : -1.70 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 850 TYR 0.026 0.001 TYR A 867 PHE 0.022 0.001 PHE A1054 TRP 0.018 0.001 TRP A1328 HIS 0.007 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00225 (10038) covalent geometry : angle 0.53897 (13594) SS BOND : bond 0.00474 ( 1) SS BOND : angle 1.55617 ( 2) hydrogen bonds : bond 0.03590 ( 497) hydrogen bonds : angle 4.02711 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.381 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 462 TRP cc_start: 0.8029 (m100) cc_final: 0.7713 (m100) REVERT: A 568 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7832 (tpt90) REVERT: A 659 GLU cc_start: 0.7870 (tt0) cc_final: 0.7633 (tt0) REVERT: A 727 LYS cc_start: 0.5983 (tttt) cc_final: 0.5637 (mtpt) REVERT: A 778 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8136 (ttmm) REVERT: A 943 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: A 969 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 1307 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 1578 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8690 (tp40) REVERT: A 1580 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6737 (tpm170) outliers start: 37 outliers final: 27 residues processed: 198 average time/residue: 0.0740 time to fit residues: 22.4949 Evaluate side-chains 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Chi-restraints excluded: chain A residue 1578 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 HIS A1381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092489 restraints weight = 20418.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095418 restraints weight = 10168.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097335 restraints weight = 6516.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098474 restraints weight = 4910.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099287 restraints weight = 4148.750| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10039 Z= 0.175 Angle : 0.589 8.476 13596 Z= 0.307 Chirality : 0.042 0.144 1525 Planarity : 0.005 0.062 1748 Dihedral : 4.458 37.211 1473 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.48 % Allowed : 18.79 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.23), residues: 1396 helix: 1.45 (0.20), residues: 680 sheet: -0.32 (0.68), residues: 71 loop : -1.75 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1505 TYR 0.018 0.002 TYR A 867 PHE 0.025 0.002 PHE A1054 TRP 0.019 0.001 TRP A1328 HIS 0.007 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00402 (10038) covalent geometry : angle 0.58840 (13594) SS BOND : bond 0.00598 ( 1) SS BOND : angle 2.35338 ( 2) hydrogen bonds : bond 0.04324 ( 497) hydrogen bonds : angle 4.16199 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.279 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 568 ARG cc_start: 0.8223 (tpt90) cc_final: 0.7895 (tpt90) REVERT: A 727 LYS cc_start: 0.6347 (tttt) cc_final: 0.5991 (mtpt) REVERT: A 778 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8057 (ttmm) REVERT: A 929 TYR cc_start: 0.8094 (m-10) cc_final: 0.7839 (m-10) REVERT: A 1307 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8111 (p) outliers start: 37 outliers final: 30 residues processed: 179 average time/residue: 0.0730 time to fit residues: 19.8835 Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 4 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 125 optimal weight: 0.1980 chunk 137 optimal weight: 8.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094854 restraints weight = 20394.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097772 restraints weight = 10255.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099696 restraints weight = 6602.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100932 restraints weight = 4996.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101693 restraints weight = 4187.907| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10039 Z= 0.122 Angle : 0.554 8.736 13596 Z= 0.286 Chirality : 0.041 0.142 1525 Planarity : 0.005 0.063 1748 Dihedral : 4.265 33.159 1473 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.03 % Allowed : 20.48 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.05 (0.23), residues: 1396 helix: 1.57 (0.20), residues: 676 sheet: -0.17 (0.70), residues: 71 loop : -1.71 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 850 TYR 0.016 0.001 TYR A 584 PHE 0.030 0.001 PHE A1054 TRP 0.035 0.001 TRP A1559 HIS 0.008 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00280 (10038) covalent geometry : angle 0.55393 (13594) SS BOND : bond 0.00600 ( 1) SS BOND : angle 1.84532 ( 2) hydrogen bonds : bond 0.03843 ( 497) hydrogen bonds : angle 4.10069 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.357 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 462 TRP cc_start: 0.8050 (m100) cc_final: 0.7679 (m100) REVERT: A 568 ARG cc_start: 0.8180 (tpt90) cc_final: 0.7859 (tpt90) REVERT: A 727 LYS cc_start: 0.6231 (tttt) cc_final: 0.5896 (mtpt) REVERT: A 1307 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8030 (p) REVERT: A 1580 ARG cc_start: 0.7175 (tpt170) cc_final: 0.6541 (tpm170) outliers start: 25 outliers final: 21 residues processed: 176 average time/residue: 0.0759 time to fit residues: 20.4781 Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1369 ASN A1381 ASN ** A1503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088675 restraints weight = 20399.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.091456 restraints weight = 10316.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093311 restraints weight = 6654.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094492 restraints weight = 5043.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095066 restraints weight = 4244.705| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10039 Z= 0.285 Angle : 0.681 10.160 13596 Z= 0.358 Chirality : 0.046 0.157 1525 Planarity : 0.005 0.063 1748 Dihedral : 4.987 42.974 1473 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.52 % Allowed : 20.00 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.33 (0.23), residues: 1396 helix: 1.20 (0.20), residues: 679 sheet: -0.76 (0.66), residues: 70 loop : -1.78 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1505 TYR 0.020 0.002 TYR A 413 PHE 0.029 0.002 PHE A1054 TRP 0.026 0.002 TRP A1559 HIS 0.007 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00651 (10038) covalent geometry : angle 0.67980 (13594) SS BOND : bond 0.00613 ( 1) SS BOND : angle 2.91843 ( 2) hydrogen bonds : bond 0.05137 ( 497) hydrogen bonds : angle 4.50115 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.432 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 727 LYS cc_start: 0.6683 (tttt) cc_final: 0.6280 (mtpt) REVERT: A 900 GLU cc_start: 0.7814 (tp30) cc_final: 0.7336 (tp30) REVERT: A 1013 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8144 (m) REVERT: A 1307 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8172 (p) outliers start: 29 outliers final: 24 residues processed: 171 average time/residue: 0.0680 time to fit residues: 17.8595 Evaluate side-chains 175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1381 ASN Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 90 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 58 optimal weight: 0.0770 chunk 52 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1090 HIS A1101 GLN A1381 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095130 restraints weight = 20248.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098121 restraints weight = 9940.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100050 restraints weight = 6261.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101284 restraints weight = 4670.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101925 restraints weight = 3896.072| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10039 Z= 0.122 Angle : 0.599 11.617 13596 Z= 0.308 Chirality : 0.041 0.180 1525 Planarity : 0.005 0.065 1748 Dihedral : 4.486 35.139 1473 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.39 % Allowed : 20.24 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.10 (0.23), residues: 1396 helix: 1.41 (0.20), residues: 680 sheet: -0.45 (0.66), residues: 73 loop : -1.72 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1505 TYR 0.017 0.001 TYR A 584 PHE 0.032 0.001 PHE A1054 TRP 0.021 0.001 TRP A1559 HIS 0.007 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00262 (10038) covalent geometry : angle 0.59889 (13594) SS BOND : bond 0.00717 ( 1) SS BOND : angle 1.94920 ( 2) hydrogen bonds : bond 0.03920 ( 497) hydrogen bonds : angle 4.18509 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.71 seconds wall clock time: 25 minutes 58.16 seconds (1558.16 seconds total)