Starting phenix.real_space_refine on Thu Sep 18 00:09:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zeq_60043/09_2025/8zeq_60043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zeq_60043/09_2025/8zeq_60043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zeq_60043/09_2025/8zeq_60043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zeq_60043/09_2025/8zeq_60043.map" model { file = "/net/cci-nas-00/data/ceres_data/8zeq_60043/09_2025/8zeq_60043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zeq_60043/09_2025/8zeq_60043.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.066 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 70 5.16 5 C 7840 2.51 5 N 2124 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12294 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1532, 12294 Classifications: {'peptide': 1532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 85, 'TRANS': 1446} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.75, per 1000 atoms: 0.22 Number of scatterers: 12294 At special positions: 0 Unit cell: (82.8, 131.56, 158.24, 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 70 16.00 O 2260 8.00 N 2124 7.00 C 7840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 482.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 38.7% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.004A pdb=" N GLN A 40 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.603A pdb=" N GLY A 138 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.766A pdb=" N CYS A 234 " --> pdb=" O HIS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 263 Processing helix chain 'A' and resid 279 through 296 removed outlier: 3.626A pdb=" N SER A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.939A pdb=" N TYR A 341 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 363 through 409 removed outlier: 3.688A pdb=" N TYR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 448 through 454 removed outlier: 4.054A pdb=" N PHE A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 532 through 547 removed outlier: 3.721A pdb=" N ALA A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 572 removed outlier: 4.275A pdb=" N ASP A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.602A pdb=" N HIS A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.621A pdb=" N MET A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 removed outlier: 4.159A pdb=" N GLU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 658 through 662' Processing helix chain 'A' and resid 698 through 716 Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 856 through 869 Processing helix chain 'A' and resid 892 through 898 removed outlier: 3.845A pdb=" N SER A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 935 through 947 removed outlier: 3.610A pdb=" N LEU A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 963 removed outlier: 3.871A pdb=" N GLY A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 975 removed outlier: 3.553A pdb=" N ASP A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 996 Processing helix chain 'A' and resid 1002 through 1025 removed outlier: 3.876A pdb=" N TYR A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1048 removed outlier: 3.620A pdb=" N LYS A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1114 Processing helix chain 'A' and resid 1116 through 1131 Processing helix chain 'A' and resid 1153 through 1168 Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 4.117A pdb=" N ASP A1173 " --> pdb=" O ASN A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1214 removed outlier: 3.891A pdb=" N VAL A1203 " --> pdb=" O PRO A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1303 removed outlier: 3.629A pdb=" N LYS A1303 " --> pdb=" O GLU A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1339 removed outlier: 3.597A pdb=" N TRP A1327 " --> pdb=" O SER A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1388 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1456 through 1470 Processing helix chain 'A' and resid 1470 through 1494 removed outlier: 3.712A pdb=" N THR A1474 " --> pdb=" O GLY A1470 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A1475 " --> pdb=" O PRO A1471 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A1476 " --> pdb=" O GLU A1472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A1494 " --> pdb=" O VAL A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1532 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 4.246A pdb=" N ARG A 610 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 9 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.795A pdb=" N THR A 45 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR A 93 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY A 104 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE A 95 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER A 102 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 100 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.767A pdb=" N VAL A 115 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS A 120 " --> pdb=" O VAL A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 213 removed outlier: 5.984A pdb=" N THR A 128 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N HIS A 159 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN A 130 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU A 129 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 431 removed outlier: 4.208A pdb=" N THR A 431 " --> pdb=" O MET A 456 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 456 " --> pdb=" O THR A 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 522 through 524 removed outlier: 3.732A pdb=" N VAL A 553 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 577 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A 622 " --> pdb=" O ARG A 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 599 through 600 removed outlier: 5.525A pdb=" N GLU A 599 " --> pdb=" O VAL A 720 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 731 through 732 removed outlier: 3.912A pdb=" N VAL A 732 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 745 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE A 847 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 775 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG A 849 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 771 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 769 removed outlier: 6.607A pdb=" N GLU A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 826 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 822 " --> pdb=" O GLU A 834 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU A 836 " --> pdb=" O GLN A 820 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN A 820 " --> pdb=" O GLU A 836 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 780 through 783 removed outlier: 3.745A pdb=" N ILE A 782 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 803 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1068 through 1070 Processing sheet with id=AB3, first strand: chain 'A' and resid 1314 through 1315 414 hydrogen bonds defined for protein. 1200 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: 1.88 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4045 1.35 - 1.46: 2908 1.46 - 1.58: 5559 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 12614 Sorted by residual: bond pdb=" CA ASN A1304 " pdb=" CB ASN A1304 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.40e+00 bond pdb=" CB ASN A1304 " pdb=" CG ASN A1304 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CB ASP A 184 " pdb=" CG ASP A 184 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.83e-01 bond pdb=" CB MET A 350 " pdb=" CG MET A 350 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.59e-01 bond pdb=" CB ASP A 541 " pdb=" CG ASP A 541 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.51e-01 ... (remaining 12609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 16893 1.70 - 3.41: 193 3.41 - 5.11: 25 5.11 - 6.82: 8 6.82 - 8.52: 3 Bond angle restraints: 17122 Sorted by residual: angle pdb=" N GLU A 674 " pdb=" CA GLU A 674 " pdb=" C GLU A 674 " ideal model delta sigma weight residual 114.56 110.88 3.68 1.27e+00 6.20e-01 8.38e+00 angle pdb=" CB MET A 350 " pdb=" CG MET A 350 " pdb=" SD MET A 350 " ideal model delta sigma weight residual 112.70 121.22 -8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" CA MET A 350 " pdb=" CB MET A 350 " pdb=" CG MET A 350 " ideal model delta sigma weight residual 114.10 119.20 -5.10 2.00e+00 2.50e-01 6.50e+00 angle pdb=" CB MET A 581 " pdb=" CG MET A 581 " pdb=" SD MET A 581 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" C LYS A1303 " pdb=" N ASN A1304 " pdb=" CA ASN A1304 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.12e+00 ... (remaining 17117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 6137 16.14 - 32.28: 934 32.28 - 48.42: 362 48.42 - 64.56: 81 64.56 - 80.70: 31 Dihedral angle restraints: 7545 sinusoidal: 3079 harmonic: 4466 Sorted by residual: dihedral pdb=" CG ARG A1315 " pdb=" CD ARG A1315 " pdb=" NE ARG A1315 " pdb=" CZ ARG A1315 " ideal model delta sinusoidal sigma weight residual -90.00 -134.73 44.73 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP A1187 " pdb=" CB ASP A1187 " pdb=" CG ASP A1187 " pdb=" OD1 ASP A1187 " ideal model delta sinusoidal sigma weight residual -30.00 -84.47 54.47 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP A1102 " pdb=" CB ASP A1102 " pdb=" CG ASP A1102 " pdb=" OD1 ASP A1102 " ideal model delta sinusoidal sigma weight residual -30.00 -83.69 53.69 1 2.00e+01 2.50e-03 9.79e+00 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1269 0.033 - 0.066: 380 0.066 - 0.099: 121 0.099 - 0.132: 66 0.132 - 0.165: 1 Chirality restraints: 1837 Sorted by residual: chirality pdb=" CA ASN A1304 " pdb=" N ASN A1304 " pdb=" C ASN A1304 " pdb=" CB ASN A1304 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE A 768 " pdb=" N ILE A 768 " pdb=" C ILE A 768 " pdb=" CB ILE A 768 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1834 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A1448 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A1449 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1449 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1449 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 763 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 764 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1220 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ARG A1220 " 0.019 2.00e-02 2.50e+03 pdb=" O ARG A1220 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A1221 " -0.006 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2622 2.78 - 3.31: 10773 3.31 - 3.84: 19597 3.84 - 4.37: 19720 4.37 - 4.90: 35867 Nonbonded interactions: 88579 Sorted by model distance: nonbonded pdb=" O LEU A1503 " pdb=" NE2 GLN A1509 " model vdw 2.255 3.120 nonbonded pdb=" O VAL A 647 " pdb=" OG SER A 654 " model vdw 2.269 3.040 nonbonded pdb=" N GLN A1031 " pdb=" OE1 GLN A1031 " model vdw 2.293 3.120 nonbonded pdb=" OH TYR A 155 " pdb=" OG SER A 656 " model vdw 2.318 3.040 nonbonded pdb=" ND2 ASN A 905 " pdb=" O VAL A1045 " model vdw 2.319 3.120 ... (remaining 88574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.490 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 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 : 0.002 0.035 12614 Z= 0.082 Angle : 0.451 8.525 17122 Z= 0.224 Chirality : 0.039 0.165 1837 Planarity : 0.003 0.051 2226 Dihedral : 18.477 80.701 4673 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 3.44 % Allowed : 33.28 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.23), residues: 1530 helix: 2.67 (0.24), residues: 518 sheet: 1.81 (0.64), residues: 83 loop : -0.51 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 898 TYR 0.009 0.000 TYR A 933 PHE 0.018 0.000 PHE A 993 TRP 0.008 0.000 TRP A1398 HIS 0.003 0.000 HIS A1316 Details of bonding type rmsd covalent geometry : bond 0.00170 (12614) covalent geometry : angle 0.45144 (17122) hydrogen bonds : bond 0.14942 ( 414) hydrogen bonds : angle 5.32569 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 125 ASP cc_start: 0.7010 (t0) cc_final: 0.6718 (t0) REVERT: A 137 LEU cc_start: 0.8100 (mt) cc_final: 0.7407 (mt) REVERT: A 164 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7343 (mm-40) REVERT: A 220 HIS cc_start: 0.5082 (OUTLIER) cc_final: 0.4309 (p-80) REVERT: A 281 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.2242 (ppp) REVERT: A 392 HIS cc_start: -0.1421 (OUTLIER) cc_final: -0.2172 (t70) REVERT: A 423 HIS cc_start: 0.6935 (m90) cc_final: 0.6656 (m90) REVERT: A 853 ASP cc_start: 0.4958 (OUTLIER) cc_final: 0.4743 (p0) REVERT: A 933 TYR cc_start: 0.5389 (p90) cc_final: 0.4244 (p90) REVERT: A 1230 MET cc_start: 0.4712 (tmm) cc_final: 0.2679 (pmm) REVERT: A 1233 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5057 (pm20) REVERT: A 1254 PHE cc_start: 0.6147 (p90) cc_final: 0.5403 (p90) REVERT: A 1450 GLU cc_start: 0.4918 (mp0) cc_final: 0.4303 (pp20) REVERT: A 1531 ASP cc_start: 0.7786 (t0) cc_final: 0.7570 (t0) outliers start: 46 outliers final: 37 residues processed: 165 average time/residue: 0.0836 time to fit residues: 21.4043 Evaluate side-chains 164 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1099 TRP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1418 ASP Chi-restraints excluded: chain A residue 1453 TRP Chi-restraints excluded: chain A residue 1485 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 97 GLN A 159 HIS A 280 HIS ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.234438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.192658 restraints weight = 17677.610| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 3.04 r_work: 0.4167 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12614 Z= 0.192 Angle : 0.672 10.137 17122 Z= 0.348 Chirality : 0.046 0.169 1837 Planarity : 0.005 0.062 2226 Dihedral : 6.838 56.859 1759 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.59 % Rotamer: Outliers : 7.18 % Allowed : 28.65 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.22), residues: 1530 helix: 1.92 (0.23), residues: 517 sheet: 0.78 (0.54), residues: 102 loop : -0.86 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.023 0.002 TYR A1006 PHE 0.028 0.002 PHE A1104 TRP 0.027 0.002 TRP A1259 HIS 0.006 0.001 HIS A1211 Details of bonding type rmsd covalent geometry : bond 0.00444 (12614) covalent geometry : angle 0.67158 (17122) hydrogen bonds : bond 0.05838 ( 414) hydrogen bonds : angle 4.28231 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 137 time to evaluate : 0.451 Fit side-chains REVERT: A 125 ASP cc_start: 0.7456 (t0) cc_final: 0.6711 (t0) REVERT: A 130 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7635 (tp-100) REVERT: A 281 MET cc_start: 0.2592 (OUTLIER) cc_final: 0.2023 (ppp) REVERT: A 392 HIS cc_start: -0.1597 (OUTLIER) cc_final: -0.2278 (t70) REVERT: A 469 ARG cc_start: 0.4968 (OUTLIER) cc_final: 0.4647 (ptt90) REVERT: A 581 MET cc_start: 0.7234 (mmp) cc_final: 0.6763 (mmm) REVERT: A 711 GLU cc_start: 0.7866 (tt0) cc_final: 0.7636 (tt0) REVERT: A 757 SER cc_start: 0.6901 (OUTLIER) cc_final: 0.6503 (p) REVERT: A 816 LYS cc_start: 0.2294 (OUTLIER) cc_final: 0.1061 (ptmm) REVERT: A 933 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6095 (p90) REVERT: A 1183 TYR cc_start: 0.5018 (OUTLIER) cc_final: 0.4202 (t80) REVERT: A 1200 LEU cc_start: 0.4782 (OUTLIER) cc_final: 0.4428 (pt) REVERT: A 1230 MET cc_start: 0.5524 (tmm) cc_final: 0.2817 (ptt) REVERT: A 1338 LEU cc_start: 0.5807 (tt) cc_final: 0.5399 (mp) REVERT: A 1450 GLU cc_start: 0.6381 (mt-10) cc_final: 0.4309 (tp30) REVERT: A 1452 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8715 (mp) REVERT: A 1463 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7663 (tp) REVERT: A 1485 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7565 (mt) REVERT: A 1494 ARG cc_start: 0.6345 (ptt90) cc_final: 0.6144 (ptt90) outliers start: 96 outliers final: 47 residues processed: 221 average time/residue: 0.0869 time to fit residues: 29.5253 Evaluate side-chains 173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 114 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1104 PHE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1162 GLN Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1364 ASP Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 149 optimal weight: 0.0980 chunk 105 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 125 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.238928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.197053 restraints weight = 17728.390| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 3.57 r_work: 0.4191 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12614 Z= 0.095 Angle : 0.489 6.933 17122 Z= 0.246 Chirality : 0.040 0.143 1837 Planarity : 0.003 0.041 2226 Dihedral : 4.898 58.321 1705 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 4.71 % Allowed : 30.74 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.22), residues: 1530 helix: 2.34 (0.23), residues: 513 sheet: 0.93 (0.56), residues: 97 loop : -0.80 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 898 TYR 0.016 0.001 TYR A1530 PHE 0.009 0.001 PHE A 848 TRP 0.010 0.001 TRP A1259 HIS 0.004 0.001 HIS A1316 Details of bonding type rmsd covalent geometry : bond 0.00207 (12614) covalent geometry : angle 0.48888 (17122) hydrogen bonds : bond 0.03318 ( 414) hydrogen bonds : angle 3.77730 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.544 Fit side-chains REVERT: A 119 ASN cc_start: 0.7663 (m-40) cc_final: 0.7451 (m-40) REVERT: A 125 ASP cc_start: 0.7417 (t0) cc_final: 0.6578 (t0) REVERT: A 237 ASN cc_start: 0.6509 (OUTLIER) cc_final: 0.6263 (m-40) REVERT: A 281 MET cc_start: 0.2579 (OUTLIER) cc_final: 0.2072 (ppp) REVERT: A 392 HIS cc_start: -0.1625 (OUTLIER) cc_final: -0.2183 (t-170) REVERT: A 469 ARG cc_start: 0.4848 (OUTLIER) cc_final: 0.4396 (ptt90) REVERT: A 581 MET cc_start: 0.7413 (mmp) cc_final: 0.7060 (mmm) REVERT: A 620 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 711 GLU cc_start: 0.8052 (tt0) cc_final: 0.7824 (pt0) REVERT: A 757 SER cc_start: 0.6867 (OUTLIER) cc_final: 0.6458 (p) REVERT: A 783 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: A 816 LYS cc_start: 0.2416 (OUTLIER) cc_final: 0.1243 (ptmm) REVERT: A 933 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.5471 (p90) REVERT: A 954 HIS cc_start: 0.4723 (OUTLIER) cc_final: 0.4372 (t-90) REVERT: A 1212 MET cc_start: 0.7828 (tpt) cc_final: 0.7626 (tpt) REVERT: A 1230 MET cc_start: 0.5371 (tmm) cc_final: 0.2793 (ptt) REVERT: A 1406 LYS cc_start: 0.7134 (tptt) cc_final: 0.6573 (pttp) REVERT: A 1450 GLU cc_start: 0.6388 (mt-10) cc_final: 0.4509 (tp30) REVERT: A 1516 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6247 (tp30) outliers start: 63 outliers final: 26 residues processed: 177 average time/residue: 0.0954 time to fit residues: 25.8407 Evaluate side-chains 147 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1104 PHE Chi-restraints excluded: chain A residue 1162 GLN Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 22 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 84 ASN A 219 ASN A 626 HIS ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.224033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.182291 restraints weight = 18275.719| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.74 r_work: 0.4023 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 12614 Z= 0.198 Angle : 0.664 12.562 17122 Z= 0.341 Chirality : 0.045 0.221 1837 Planarity : 0.005 0.054 2226 Dihedral : 5.345 56.852 1698 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.29 % Rotamer: Outliers : 6.36 % Allowed : 28.87 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1530 helix: 1.82 (0.23), residues: 511 sheet: 0.18 (0.50), residues: 126 loop : -1.13 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1000 TYR 0.020 0.002 TYR A 512 PHE 0.026 0.002 PHE A1104 TRP 0.019 0.002 TRP A 208 HIS 0.005 0.001 HIS A1211 Details of bonding type rmsd covalent geometry : bond 0.00466 (12614) covalent geometry : angle 0.66434 (17122) hydrogen bonds : bond 0.05867 ( 414) hydrogen bonds : angle 4.35641 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 131 time to evaluate : 0.321 Fit side-chains REVERT: A 27 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7158 (mt0) REVERT: A 163 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8124 (mt) REVERT: A 220 HIS cc_start: 0.4814 (OUTLIER) cc_final: 0.3887 (p-80) REVERT: A 281 MET cc_start: 0.2365 (OUTLIER) cc_final: 0.1862 (ppp) REVERT: A 316 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.4777 (tt) REVERT: A 392 HIS cc_start: -0.1349 (OUTLIER) cc_final: -0.2084 (t-170) REVERT: A 469 ARG cc_start: 0.5488 (OUTLIER) cc_final: 0.5112 (ptt90) REVERT: A 581 MET cc_start: 0.8081 (mmp) cc_final: 0.7684 (mmt) REVERT: A 620 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8172 (mp) REVERT: A 711 GLU cc_start: 0.7857 (tt0) cc_final: 0.7596 (pt0) REVERT: A 757 SER cc_start: 0.7180 (OUTLIER) cc_final: 0.6583 (p) REVERT: A 783 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: A 809 HIS cc_start: 0.6293 (OUTLIER) cc_final: 0.5908 (m-70) REVERT: A 816 LYS cc_start: 0.3779 (OUTLIER) cc_final: 0.2334 (ptmm) REVERT: A 933 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.5766 (p90) REVERT: A 954 HIS cc_start: 0.5126 (OUTLIER) cc_final: 0.4765 (t-90) REVERT: A 1183 TYR cc_start: 0.5525 (OUTLIER) cc_final: 0.4028 (t80) REVERT: A 1230 MET cc_start: 0.5741 (tmm) cc_final: 0.3313 (ptt) REVERT: A 1237 ILE cc_start: 0.3913 (mm) cc_final: 0.3634 (mm) REVERT: A 1406 LYS cc_start: 0.7471 (tptt) cc_final: 0.6766 (pttp) REVERT: A 1450 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.4810 (tp30) REVERT: A 1531 ASP cc_start: 0.8027 (t0) cc_final: 0.7765 (t0) outliers start: 85 outliers final: 44 residues processed: 205 average time/residue: 0.1002 time to fit residues: 30.8077 Evaluate side-chains 170 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 110 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1104 PHE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1450 GLU Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1497 TRP Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 0.0050 chunk 58 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 237 ASN A 547 GLN A 618 HIS A 626 HIS A 857 GLN A 905 ASN A1133 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.228015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.187580 restraints weight = 18395.145| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.76 r_work: 0.4080 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12614 Z= 0.112 Angle : 0.532 9.053 17122 Z= 0.269 Chirality : 0.041 0.133 1837 Planarity : 0.003 0.037 2226 Dihedral : 4.885 57.459 1698 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.49 % Favored : 94.38 % Rotamer: Outliers : 5.01 % Allowed : 30.44 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1530 helix: 2.20 (0.23), residues: 509 sheet: 0.15 (0.51), residues: 121 loop : -1.14 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 898 TYR 0.023 0.001 TYR A1530 PHE 0.010 0.001 PHE A1104 TRP 0.011 0.001 TRP A 680 HIS 0.004 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00253 (12614) covalent geometry : angle 0.53186 (17122) hydrogen bonds : bond 0.03655 ( 414) hydrogen bonds : angle 3.91180 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 112 time to evaluate : 0.471 Fit side-chains REVERT: A 125 ASP cc_start: 0.7526 (t0) cc_final: 0.7083 (t0) REVERT: A 163 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 220 HIS cc_start: 0.4519 (OUTLIER) cc_final: 0.3283 (p-80) REVERT: A 281 MET cc_start: 0.2602 (OUTLIER) cc_final: 0.2107 (ppp) REVERT: A 392 HIS cc_start: -0.1931 (OUTLIER) cc_final: -0.2871 (t-170) REVERT: A 456 MET cc_start: 0.6724 (mmt) cc_final: 0.5995 (mmt) REVERT: A 469 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.4938 (ptt90) REVERT: A 539 MET cc_start: 0.7012 (mmt) cc_final: 0.6788 (mmt) REVERT: A 581 MET cc_start: 0.8072 (mmp) cc_final: 0.7771 (mmt) REVERT: A 620 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 711 GLU cc_start: 0.7933 (tt0) cc_final: 0.7637 (pt0) REVERT: A 757 SER cc_start: 0.7141 (OUTLIER) cc_final: 0.6580 (p) REVERT: A 783 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: A 801 ASP cc_start: 0.7937 (p0) cc_final: 0.7588 (p0) REVERT: A 816 LYS cc_start: 0.4057 (OUTLIER) cc_final: 0.2619 (ptmm) REVERT: A 933 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5834 (p90) REVERT: A 954 HIS cc_start: 0.4808 (OUTLIER) cc_final: 0.4528 (t-90) REVERT: A 1183 TYR cc_start: 0.5408 (OUTLIER) cc_final: 0.3942 (t80) REVERT: A 1200 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4757 (pt) REVERT: A 1209 GLN cc_start: 0.6497 (tp40) cc_final: 0.6088 (mt0) REVERT: A 1230 MET cc_start: 0.5754 (tmm) cc_final: 0.2793 (ptt) REVERT: A 1285 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: A 1406 LYS cc_start: 0.7134 (tptt) cc_final: 0.6625 (pttp) REVERT: A 1485 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7209 (mt) REVERT: A 1531 ASP cc_start: 0.7925 (t0) cc_final: 0.7596 (t0) outliers start: 67 outliers final: 39 residues processed: 170 average time/residue: 0.0995 time to fit residues: 25.4617 Evaluate side-chains 159 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1104 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1256 CYS Chi-restraints excluded: chain A residue 1282 SER Chi-restraints excluded: chain A residue 1285 GLU Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1497 TRP Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 140 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 137 optimal weight: 0.0030 chunk 126 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 GLN A1209 GLN A1309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.226553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.185524 restraints weight = 18311.597| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 3.86 r_work: 0.4061 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12614 Z= 0.112 Angle : 0.527 9.478 17122 Z= 0.266 Chirality : 0.041 0.146 1837 Planarity : 0.004 0.037 2226 Dihedral : 4.796 57.479 1698 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.67 % Favored : 93.20 % Rotamer: Outliers : 5.91 % Allowed : 29.62 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1530 helix: 2.18 (0.23), residues: 516 sheet: -0.02 (0.50), residues: 121 loop : -1.17 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 898 TYR 0.018 0.001 TYR A1530 PHE 0.014 0.001 PHE A1104 TRP 0.009 0.001 TRP A1398 HIS 0.004 0.001 HIS A1316 Details of bonding type rmsd covalent geometry : bond 0.00256 (12614) covalent geometry : angle 0.52726 (17122) hydrogen bonds : bond 0.03764 ( 414) hydrogen bonds : angle 3.80664 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 117 time to evaluate : 0.520 Fit side-chains REVERT: A 125 ASP cc_start: 0.7618 (t0) cc_final: 0.7183 (t0) REVERT: A 220 HIS cc_start: 0.4490 (OUTLIER) cc_final: 0.3233 (p-80) REVERT: A 281 MET cc_start: 0.2541 (OUTLIER) cc_final: 0.2068 (ppp) REVERT: A 392 HIS cc_start: -0.2105 (OUTLIER) cc_final: -0.3073 (t-170) REVERT: A 469 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.5034 (ptt90) REVERT: A 620 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 711 GLU cc_start: 0.8018 (tt0) cc_final: 0.7616 (pt0) REVERT: A 723 ASP cc_start: 0.7902 (p0) cc_final: 0.7306 (t70) REVERT: A 757 SER cc_start: 0.7012 (OUTLIER) cc_final: 0.6454 (p) REVERT: A 783 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: A 801 ASP cc_start: 0.7986 (p0) cc_final: 0.7621 (p0) REVERT: A 816 LYS cc_start: 0.3972 (OUTLIER) cc_final: 0.2508 (ptmm) REVERT: A 933 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.5686 (p90) REVERT: A 954 HIS cc_start: 0.4931 (OUTLIER) cc_final: 0.4664 (t-90) REVERT: A 1183 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.3943 (t80) REVERT: A 1200 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.4964 (pt) REVERT: A 1209 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.6114 (mt0) REVERT: A 1230 MET cc_start: 0.5487 (tmm) cc_final: 0.2770 (ptt) REVERT: A 1285 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: A 1531 ASP cc_start: 0.7920 (t0) cc_final: 0.7645 (t0) outliers start: 79 outliers final: 48 residues processed: 186 average time/residue: 0.0889 time to fit residues: 25.6684 Evaluate side-chains 166 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 104 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1104 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1256 CYS Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1282 SER Chi-restraints excluded: chain A residue 1285 GLU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1365 SER Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1497 TRP Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1133 HIS A1209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.226050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.185420 restraints weight = 17591.948| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 3.46 r_work: 0.4065 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12614 Z= 0.110 Angle : 0.534 9.174 17122 Z= 0.269 Chirality : 0.041 0.137 1837 Planarity : 0.004 0.044 2226 Dihedral : 4.855 57.915 1698 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 5.24 % Allowed : 30.07 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1530 helix: 2.19 (0.23), residues: 516 sheet: -0.09 (0.49), residues: 127 loop : -1.18 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 910 TYR 0.019 0.001 TYR A1530 PHE 0.012 0.001 PHE A1104 TRP 0.011 0.001 TRP A 928 HIS 0.004 0.001 HIS A1316 Details of bonding type rmsd covalent geometry : bond 0.00249 (12614) covalent geometry : angle 0.53422 (17122) hydrogen bonds : bond 0.03545 ( 414) hydrogen bonds : angle 3.77211 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 112 time to evaluate : 0.468 Fit side-chains REVERT: A 112 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7370 (pt) REVERT: A 125 ASP cc_start: 0.7615 (t0) cc_final: 0.7193 (t0) REVERT: A 220 HIS cc_start: 0.4463 (OUTLIER) cc_final: 0.3240 (p-80) REVERT: A 281 MET cc_start: 0.2600 (OUTLIER) cc_final: 0.2126 (ppp) REVERT: A 392 HIS cc_start: -0.2213 (OUTLIER) cc_final: -0.3204 (t-170) REVERT: A 469 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.5036 (ptt90) REVERT: A 620 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 711 GLU cc_start: 0.7924 (tt0) cc_final: 0.7549 (pt0) REVERT: A 723 ASP cc_start: 0.7813 (p0) cc_final: 0.7274 (t70) REVERT: A 757 SER cc_start: 0.7026 (OUTLIER) cc_final: 0.6462 (p) REVERT: A 783 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: A 801 ASP cc_start: 0.7939 (p0) cc_final: 0.7624 (p0) REVERT: A 816 LYS cc_start: 0.3972 (OUTLIER) cc_final: 0.2497 (ptmm) REVERT: A 933 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5866 (p90) REVERT: A 954 HIS cc_start: 0.4938 (OUTLIER) cc_final: 0.4688 (t-90) REVERT: A 1008 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6581 (t0) REVERT: A 1183 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.3943 (t80) REVERT: A 1200 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5252 (pt) REVERT: A 1209 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6325 (mt0) REVERT: A 1230 MET cc_start: 0.5485 (tmm) cc_final: 0.2823 (ptt) REVERT: A 1285 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: A 1422 MET cc_start: 0.4023 (pmm) cc_final: 0.1961 (mpp) REVERT: A 1502 GLU cc_start: 0.5832 (mt-10) cc_final: 0.5373 (mt-10) outliers start: 70 outliers final: 47 residues processed: 171 average time/residue: 0.0939 time to fit residues: 25.0432 Evaluate side-chains 168 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 105 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1104 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1256 CYS Chi-restraints excluded: chain A residue 1282 SER Chi-restraints excluded: chain A residue 1285 GLU Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1497 TRP Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 chunk 20 optimal weight: 2.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 869 GLN A1205 GLN A1209 GLN A1505 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.215920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.174785 restraints weight = 17924.472| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 3.25 r_work: 0.3960 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12614 Z= 0.211 Angle : 0.695 11.019 17122 Z= 0.361 Chirality : 0.047 0.185 1837 Planarity : 0.005 0.066 2226 Dihedral : 5.807 58.449 1698 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.22 % Favored : 90.65 % Rotamer: Outliers : 6.06 % Allowed : 28.95 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.22), residues: 1530 helix: 1.47 (0.23), residues: 527 sheet: -0.47 (0.46), residues: 144 loop : -1.57 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1116 TYR 0.024 0.002 TYR A 512 PHE 0.027 0.002 PHE A1104 TRP 0.026 0.002 TRP A1023 HIS 0.008 0.001 HIS A1309 Details of bonding type rmsd covalent geometry : bond 0.00496 (12614) covalent geometry : angle 0.69533 (17122) hydrogen bonds : bond 0.06365 ( 414) hydrogen bonds : angle 4.43939 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 117 time to evaluate : 0.495 Fit side-chains REVERT: A 112 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7775 (mt) REVERT: A 220 HIS cc_start: 0.4578 (OUTLIER) cc_final: 0.3257 (p-80) REVERT: A 224 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7155 (p0) REVERT: A 281 MET cc_start: 0.2531 (OUTLIER) cc_final: 0.2080 (ppp) REVERT: A 392 HIS cc_start: -0.2692 (OUTLIER) cc_final: -0.3619 (t-170) REVERT: A 539 MET cc_start: 0.7421 (mmt) cc_final: 0.7094 (mmt) REVERT: A 565 ASN cc_start: 0.8437 (m-40) cc_final: 0.8212 (m110) REVERT: A 620 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 711 GLU cc_start: 0.7796 (tt0) cc_final: 0.7531 (pt0) REVERT: A 723 ASP cc_start: 0.8107 (p0) cc_final: 0.7769 (t0) REVERT: A 759 TYR cc_start: 0.5900 (m-80) cc_final: 0.5522 (m-80) REVERT: A 933 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6116 (p90) REVERT: A 954 HIS cc_start: 0.5160 (OUTLIER) cc_final: 0.4795 (t-90) REVERT: A 1183 TYR cc_start: 0.5642 (OUTLIER) cc_final: 0.3975 (t80) REVERT: A 1200 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.5089 (pt) REVERT: A 1230 MET cc_start: 0.5914 (tmm) cc_final: 0.3195 (ptt) REVERT: A 1285 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: A 1420 ASP cc_start: 0.7635 (p0) cc_final: 0.6681 (m-30) REVERT: A 1422 MET cc_start: 0.4767 (pmm) cc_final: 0.2967 (mpp) outliers start: 81 outliers final: 53 residues processed: 187 average time/residue: 0.0961 time to fit residues: 27.6479 Evaluate side-chains 170 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 106 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1256 CYS Chi-restraints excluded: chain A residue 1282 SER Chi-restraints excluded: chain A residue 1285 GLU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1365 SER Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1497 TRP Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 76 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 833 GLN A1133 HIS A1213 GLN A1509 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.221907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180871 restraints weight = 18389.856| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 3.37 r_work: 0.4033 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12614 Z= 0.120 Angle : 0.577 9.745 17122 Z= 0.292 Chirality : 0.042 0.137 1837 Planarity : 0.004 0.047 2226 Dihedral : 5.059 59.149 1694 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.80 % Favored : 93.07 % Rotamer: Outliers : 4.26 % Allowed : 30.67 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1530 helix: 1.87 (0.23), residues: 517 sheet: -0.63 (0.48), residues: 127 loop : -1.45 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 481 TYR 0.023 0.001 TYR A1530 PHE 0.016 0.001 PHE A 837 TRP 0.023 0.001 TRP A 487 HIS 0.007 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00269 (12614) covalent geometry : angle 0.57714 (17122) hydrogen bonds : bond 0.03843 ( 414) hydrogen bonds : angle 3.95410 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 0.471 Fit side-chains REVERT: A 125 ASP cc_start: 0.7688 (t0) cc_final: 0.7336 (t0) REVERT: A 220 HIS cc_start: 0.4341 (OUTLIER) cc_final: 0.3075 (p-80) REVERT: A 281 MET cc_start: 0.2613 (OUTLIER) cc_final: 0.2206 (ppp) REVERT: A 392 HIS cc_start: -0.2340 (OUTLIER) cc_final: -0.3395 (t-170) REVERT: A 456 MET cc_start: 0.6648 (mmt) cc_final: 0.5981 (mmt) REVERT: A 463 MET cc_start: 0.4531 (mpp) cc_final: 0.3820 (mpp) REVERT: A 620 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 711 GLU cc_start: 0.7927 (tt0) cc_final: 0.7558 (pt0) REVERT: A 723 ASP cc_start: 0.7963 (p0) cc_final: 0.7515 (t0) REVERT: A 801 ASP cc_start: 0.7935 (p0) cc_final: 0.7674 (p0) REVERT: A 933 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6189 (p90) REVERT: A 1183 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.3951 (t80) REVERT: A 1209 GLN cc_start: 0.7178 (tp40) cc_final: 0.6901 (tt0) REVERT: A 1230 MET cc_start: 0.5636 (tmm) cc_final: 0.2930 (ptt) REVERT: A 1285 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: A 1420 ASP cc_start: 0.7766 (p0) cc_final: 0.6782 (m-30) REVERT: A 1422 MET cc_start: 0.4642 (pmm) cc_final: 0.2662 (tpp) REVERT: A 1502 GLU cc_start: 0.6100 (mt-10) cc_final: 0.5759 (mt-10) outliers start: 57 outliers final: 42 residues processed: 161 average time/residue: 0.0781 time to fit residues: 19.8914 Evaluate side-chains 156 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1256 CYS Chi-restraints excluded: chain A residue 1282 SER Chi-restraints excluded: chain A residue 1285 GLU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1365 SER Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1497 TRP Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 71 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.220813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.178894 restraints weight = 18396.799| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 3.39 r_work: 0.4023 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12614 Z= 0.124 Angle : 0.578 9.498 17122 Z= 0.292 Chirality : 0.042 0.143 1837 Planarity : 0.004 0.037 2226 Dihedral : 5.034 59.755 1692 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.12 % Favored : 92.81 % Rotamer: Outliers : 3.74 % Allowed : 31.26 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.22), residues: 1530 helix: 1.87 (0.23), residues: 522 sheet: -0.60 (0.48), residues: 129 loop : -1.46 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 481 TYR 0.022 0.001 TYR A1530 PHE 0.014 0.001 PHE A 837 TRP 0.020 0.001 TRP A 487 HIS 0.009 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00284 (12614) covalent geometry : angle 0.57788 (17122) hydrogen bonds : bond 0.04023 ( 414) hydrogen bonds : angle 3.92558 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.475 Fit side-chains REVERT: A 125 ASP cc_start: 0.7650 (t0) cc_final: 0.7368 (t0) REVERT: A 220 HIS cc_start: 0.4357 (OUTLIER) cc_final: 0.3142 (p-80) REVERT: A 281 MET cc_start: 0.2534 (OUTLIER) cc_final: 0.2107 (ppp) REVERT: A 461 TRP cc_start: 0.4227 (p90) cc_final: 0.3996 (p90) REVERT: A 539 MET cc_start: 0.7220 (mmt) cc_final: 0.6950 (mmt) REVERT: A 620 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7914 (mp) REVERT: A 711 GLU cc_start: 0.7890 (tt0) cc_final: 0.7543 (pt0) REVERT: A 723 ASP cc_start: 0.7914 (p0) cc_final: 0.7519 (t0) REVERT: A 801 ASP cc_start: 0.7982 (p0) cc_final: 0.7738 (p0) REVERT: A 933 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6118 (p90) REVERT: A 954 HIS cc_start: 0.4824 (OUTLIER) cc_final: 0.4566 (t-90) REVERT: A 1064 MET cc_start: 0.6034 (ttt) cc_final: 0.5798 (ptm) REVERT: A 1183 TYR cc_start: 0.5558 (OUTLIER) cc_final: 0.3952 (t80) REVERT: A 1230 MET cc_start: 0.5702 (tmm) cc_final: 0.2901 (ptt) REVERT: A 1285 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 1420 ASP cc_start: 0.7602 (p0) cc_final: 0.6732 (m-30) REVERT: A 1422 MET cc_start: 0.4830 (pmm) cc_final: 0.2882 (tpp) REVERT: A 1502 GLU cc_start: 0.5903 (mt-10) cc_final: 0.5545 (mt-10) outliers start: 50 outliers final: 41 residues processed: 155 average time/residue: 0.0892 time to fit residues: 21.8080 Evaluate side-chains 158 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1183 TYR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1282 SER Chi-restraints excluded: chain A residue 1285 GLU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1365 SER Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1497 TRP Chi-restraints excluded: chain A residue 1518 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 GLN A1209 GLN ** A1518 GLN ** 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 = 0.4568 r_free = 0.4568 target = 0.215455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.174136 restraints weight = 18171.821| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.50 r_work: 0.3944 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12614 Z= 0.174 Angle : 0.654 10.381 17122 Z= 0.336 Chirality : 0.045 0.174 1837 Planarity : 0.005 0.053 2226 Dihedral : 5.424 71.386 1690 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.76 % Favored : 91.18 % Rotamer: Outliers : 4.56 % Allowed : 30.29 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.22), residues: 1530 helix: 1.62 (0.23), residues: 523 sheet: -0.79 (0.48), residues: 131 loop : -1.57 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1116 TYR 0.024 0.002 TYR A1530 PHE 0.025 0.002 PHE A 892 TRP 0.024 0.002 TRP A1023 HIS 0.011 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00406 (12614) covalent geometry : angle 0.65382 (17122) hydrogen bonds : bond 0.05534 ( 414) hydrogen bonds : angle 4.21402 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3154.62 seconds wall clock time: 54 minutes 43.44 seconds (3283.44 seconds total)