Starting phenix.real_space_refine on Thu Aug 6 00:57:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9edb_47943/08_2026/9edb_47943.cif Found real_map, /net/cci-nas-00/data/ceres_data/9edb_47943/08_2026/9edb_47943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9edb_47943/08_2026/9edb_47943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9edb_47943/08_2026/9edb_47943.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9edb_47943/08_2026/9edb_47943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9edb_47943/08_2026/9edb_47943.map" } resolution = 3.1 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 122 5.49 5 S 20 5.16 5 C 7595 2.51 5 N 2239 2.21 5 O 2660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12636 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10049 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1342, 10049 Classifications: {'peptide': 1342} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 35, 'TRANS': 1306} Chain breaks: 4 Unresolved non-hydrogen bonds: 948 Unresolved non-hydrogen angles: 1163 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ASP:plan': 28, 'GLU:plan': 49, 'ASN:plan1': 16, 'ARG:plan': 18, 'GLN:plan1': 12, 'TYR:plan': 5, 'PHE:plan': 4, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 529 Chain: "B" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1909 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 77} Chain: "C" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 3.23, per 1000 atoms: 0.26 Number of scatterers: 12636 At special positions: 0 Unit cell: (99.1508, 127.48, 124.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 122 15.00 O 2660 8.00 N 2239 7.00 C 7595 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: 0.83 Conformation dependent library (CDL) restraints added in 495.0 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 53.9% alpha, 7.2% beta 39 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.247A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.950A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.773A pdb=" N LEU A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.518A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.990A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.322A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.861A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.659A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.754A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 557 removed outlier: 4.730A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.795A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.529A pdb=" N VAL A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.602A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.709A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 792 Processing helix chain 'A' and resid 802 through 806 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.737A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.073A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.592A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.997A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.505A pdb=" N ILE A1022 " --> pdb=" O VAL A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1075 through 1088 removed outlier: 3.669A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.089A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.842A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.643A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 removed outlier: 3.784A pdb=" N GLU A1307 " --> pdb=" O ARG A1303 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1341 through 1344 removed outlier: 3.720A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1341 through 1344' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 3.672A pdb=" N ILE A 759 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 956 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.082A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 removed outlier: 4.793A pdb=" N THR A 466 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 509 removed outlier: 4.863A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 560 removed outlier: 4.050A pdb=" N VAL A 559 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA8, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA9, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB1, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.539A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1324 through 1325 498 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3108 1.33 - 1.46: 3394 1.46 - 1.58: 6345 1.58 - 1.70: 242 1.70 - 1.82: 38 Bond restraints: 13127 Sorted by residual: bond pdb=" C3' DC C -2 " pdb=" O3' DC C -2 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" C3' DT D 44 " pdb=" C2' DT D 44 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DC D 38 " pdb=" C2' DC D 38 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.41e+00 bond pdb=" C1' DT C 0 " pdb=" N1 DT C 0 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.88e+00 bond pdb=" C3' DT C 0 " pdb=" C2' DT C 0 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.63e+00 ... (remaining 13122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 18091 3.15 - 6.30: 213 6.30 - 9.45: 38 9.45 - 12.59: 8 12.59 - 15.74: 1 Bond angle restraints: 18351 Sorted by residual: angle pdb=" C1' C B 60 " pdb=" N1 C B 60 " pdb=" C2 C B 60 " ideal model delta sigma weight residual 118.80 125.80 -7.00 1.10e+00 8.26e-01 4.05e+01 angle pdb=" C1' C B 18 " pdb=" N1 C B 18 " pdb=" C2 C B 18 " ideal model delta sigma weight residual 118.80 125.72 -6.92 1.10e+00 8.26e-01 3.96e+01 angle pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sigma weight residual 118.80 125.63 -6.83 1.10e+00 8.26e-01 3.85e+01 angle pdb=" CA LYS A1085 " pdb=" CB LYS A1085 " pdb=" CG LYS A1085 " ideal model delta sigma weight residual 114.10 126.45 -12.35 2.00e+00 2.50e-01 3.81e+01 angle pdb=" CA LYS A 710 " pdb=" CB LYS A 710 " pdb=" CG LYS A 710 " ideal model delta sigma weight residual 114.10 126.04 -11.94 2.00e+00 2.50e-01 3.56e+01 ... (remaining 18346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 7367 34.47 - 68.95: 483 68.95 - 103.42: 26 103.42 - 137.90: 0 137.90 - 172.37: 4 Dihedral angle restraints: 7880 sinusoidal: 3941 harmonic: 3939 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 37.21 162.79 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U B 56 " pdb=" C1' U B 56 " pdb=" N1 U B 56 " pdb=" C2 U B 56 " ideal model delta sinusoidal sigma weight residual -128.00 -66.96 -61.04 1 1.70e+01 3.46e-03 1.71e+01 dihedral pdb=" CA PHE A 972 " pdb=" C PHE A 972 " pdb=" N TYR A 973 " pdb=" CA TYR A 973 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1734 0.063 - 0.127: 349 0.127 - 0.190: 75 0.190 - 0.254: 6 0.254 - 0.317: 3 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CG LEU A 423 " pdb=" CB LEU A 423 " pdb=" CD1 LEU A 423 " pdb=" CD2 LEU A 423 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU A 433 " pdb=" CB LEU A 433 " pdb=" CD1 LEU A 433 " pdb=" CD2 LEU A 433 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2164 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 435 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" CG ASP A 435 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASP A 435 " -0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP A 435 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 271 " 0.017 2.00e-02 2.50e+03 2.36e-02 1.12e+01 pdb=" CG TYR A 271 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 271 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 271 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 271 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 271 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 271 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 271 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 973 " 0.023 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR A 973 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 973 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 973 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 973 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 973 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 973 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 973 " -0.001 2.00e-02 2.50e+03 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2618 2.78 - 3.31: 11220 3.31 - 3.84: 22344 3.84 - 4.37: 25227 4.37 - 4.90: 40420 Nonbonded interactions: 101829 Sorted by model distance: nonbonded pdb=" O SER A1136 " pdb=" OG SER A1136 " model vdw 2.248 3.040 nonbonded pdb=" O LYS A 209 " pdb=" OG SER A 213 " model vdw 2.288 3.040 nonbonded pdb=" OG SER A 909 " pdb=" OD2 ASP A 912 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.311 3.040 nonbonded pdb=" O ILE A 305 " pdb=" OG SER A 320 " model vdw 2.313 3.040 ... (remaining 101824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.005 0.064 13127 Z= 0.312 Angle : 0.956 15.744 18351 Z= 0.621 Chirality : 0.055 0.317 2167 Planarity : 0.006 0.068 1912 Dihedral : 19.800 172.371 5328 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.53 % Allowed : 21.82 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.21), residues: 1332 helix: -0.86 (0.19), residues: 671 sheet: -0.84 (0.50), residues: 110 loop : -2.00 (0.22), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 457 TYR 0.056 0.003 TYR A 271 PHE 0.042 0.003 PHE A 643 TRP 0.014 0.002 TRP A 659 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.31 (13127) covalent geometry : angle 0.95610 / 0.62 (18351) hydrogen bonds : bond 0.14612 / 9.79 ( 595) hydrogen bonds : angle 6.44790 / 4.68 ( 1633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8794 (ttp-170) cc_final: 0.8277 (ttp-170) REVERT: A 223 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7314 (pt0) REVERT: A 235 ASN cc_start: 0.8441 (m-40) cc_final: 0.7651 (t0) REVERT: A 258 LEU cc_start: 0.7965 (mm) cc_final: 0.7757 (mt) REVERT: A 395 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7202 (ttp80) REVERT: A 662 LEU cc_start: 0.7946 (mm) cc_final: 0.7707 (mm) REVERT: A 895 ARG cc_start: 0.6475 (mtp180) cc_final: 0.6183 (tpt170) REVERT: A 919 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7562 (ttt180) REVERT: A 935 LEU cc_start: 0.9136 (mt) cc_final: 0.8857 (mp) REVERT: A 1108 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8696 (mt-10) outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 0.0988 time to fit residues: 19.1950 Evaluate side-chains 114 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 404 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 8.9990 overall best weight: 0.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 ASN A1308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.119280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083307 restraints weight = 25930.953| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.58 r_work: 0.3085 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13127 Z= 0.149 Angle : 0.588 12.344 18351 Z= 0.320 Chirality : 0.041 0.296 2167 Planarity : 0.004 0.051 1912 Dihedral : 20.467 176.623 3152 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.21 % Allowed : 17.86 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1332 helix: 0.14 (0.20), residues: 676 sheet: -0.92 (0.46), residues: 123 loop : -1.75 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1078 TYR 0.023 0.001 TYR A 639 PHE 0.016 0.001 PHE A 432 TRP 0.019 0.002 TRP A1074 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (13127) covalent geometry : angle 0.58768 / 0.32 (18351) hydrogen bonds : bond 0.04870 / 3.30 ( 595) hydrogen bonds : angle 4.88642 / 3.52 ( 1633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8743 (ttp-170) cc_final: 0.8533 (ttp-170) REVERT: A 235 ASN cc_start: 0.8523 (m-40) cc_final: 0.7732 (t0) REVERT: A 258 LEU cc_start: 0.7964 (mm) cc_final: 0.7744 (mt) REVERT: A 394 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7834 (m110) REVERT: A 493 GLU cc_start: 0.8437 (pp20) cc_final: 0.8113 (pp20) REVERT: A 662 LEU cc_start: 0.8027 (mm) cc_final: 0.7809 (mm) REVERT: A 895 ARG cc_start: 0.6471 (mtp180) cc_final: 0.6094 (tpt170) REVERT: A 919 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7582 (ttm170) REVERT: A 1108 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8739 (mt-10) REVERT: A 1194 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8701 (mp) outliers start: 30 outliers final: 13 residues processed: 137 average time/residue: 0.0860 time to fit residues: 17.5258 Evaluate side-chains 119 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN ** A 595 HIS ** 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 = 0.3755 r_free = 0.3755 target = 0.115327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.077829 restraints weight = 26187.527| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.57 r_work: 0.2991 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13127 Z= 0.213 Angle : 0.602 11.823 18351 Z= 0.324 Chirality : 0.042 0.289 2167 Planarity : 0.004 0.054 1912 Dihedral : 20.493 177.687 3152 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.32 % Allowed : 17.22 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.22), residues: 1332 helix: 0.55 (0.20), residues: 675 sheet: -1.09 (0.45), residues: 127 loop : -1.55 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 653 TYR 0.017 0.002 TYR A 155 PHE 0.020 0.002 PHE A1235 TRP 0.013 0.001 TRP A1074 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (13127) covalent geometry : angle 0.60184 / 0.32 (18351) hydrogen bonds : bond 0.04757 / 3.21 ( 595) hydrogen bonds : angle 4.50833 / 3.24 ( 1633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8856 (ttp-170) cc_final: 0.8589 (ttp-170) REVERT: A 235 ASN cc_start: 0.8510 (m-40) cc_final: 0.7722 (t0) REVERT: A 258 LEU cc_start: 0.8022 (mm) cc_final: 0.7807 (mt) REVERT: A 493 GLU cc_start: 0.8536 (pp20) cc_final: 0.8275 (pp20) REVERT: A 605 ASP cc_start: 0.8820 (t0) cc_final: 0.8245 (p0) REVERT: A 895 ARG cc_start: 0.6562 (mtp180) cc_final: 0.6160 (tpt170) REVERT: A 919 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7631 (ttm170) REVERT: A 1108 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8771 (mt-10) REVERT: A 1194 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8697 (mp) outliers start: 31 outliers final: 20 residues processed: 132 average time/residue: 0.0918 time to fit residues: 18.2609 Evaluate side-chains 117 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 75 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 103 optimal weight: 0.0030 chunk 128 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 412 HIS A 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.116814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079721 restraints weight = 25959.518| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.57 r_work: 0.3037 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 13127 Z= 0.112 Angle : 0.504 12.067 18351 Z= 0.276 Chirality : 0.038 0.286 2167 Planarity : 0.003 0.046 1912 Dihedral : 20.449 176.970 3150 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.67 % Allowed : 19.68 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1332 helix: 0.87 (0.20), residues: 674 sheet: -0.96 (0.46), residues: 125 loop : -1.43 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.013 0.001 TYR A 639 PHE 0.013 0.001 PHE A 432 TRP 0.012 0.001 TRP A1074 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (13127) covalent geometry : angle 0.50379 / 0.28 (18351) hydrogen bonds : bond 0.03995 / 2.69 ( 595) hydrogen bonds : angle 4.32704 / 3.14 ( 1633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8868 (ttp-170) cc_final: 0.8612 (ttp-170) REVERT: A 235 ASN cc_start: 0.8451 (m-40) cc_final: 0.7673 (t0) REVERT: A 258 LEU cc_start: 0.8024 (mm) cc_final: 0.7821 (mt) REVERT: A 493 GLU cc_start: 0.8465 (pp20) cc_final: 0.8177 (pp20) REVERT: A 605 ASP cc_start: 0.8815 (t0) cc_final: 0.8262 (p0) REVERT: A 746 GLU cc_start: 0.8582 (tt0) cc_final: 0.8305 (tt0) REVERT: A 895 ARG cc_start: 0.6541 (mtp180) cc_final: 0.6141 (tpt170) REVERT: A 919 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7604 (ttm170) REVERT: A 1108 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8717 (mt-10) REVERT: A 1194 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8645 (mp) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.0968 time to fit residues: 17.5460 Evaluate side-chains 113 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain A residue 1270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 0.0470 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 281 GLN A 511 HIS ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078901 restraints weight = 26209.507| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.58 r_work: 0.3023 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13127 Z= 0.128 Angle : 0.499 11.654 18351 Z= 0.273 Chirality : 0.038 0.284 2167 Planarity : 0.003 0.047 1912 Dihedral : 20.322 177.270 3150 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.42 % Allowed : 19.04 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1332 helix: 1.08 (0.21), residues: 675 sheet: -0.89 (0.46), residues: 125 loop : -1.30 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.014 0.001 TYR A1131 PHE 0.013 0.001 PHE A 432 TRP 0.009 0.001 TRP A1074 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (13127) covalent geometry : angle 0.49940 / 0.27 (18351) hydrogen bonds : bond 0.03855 / 2.60 ( 595) hydrogen bonds : angle 4.21014 / 3.04 ( 1633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8881 (ttp-170) cc_final: 0.8607 (ttp-170) REVERT: A 493 GLU cc_start: 0.8504 (pp20) cc_final: 0.8174 (pp20) REVERT: A 605 ASP cc_start: 0.8816 (t0) cc_final: 0.8246 (p0) REVERT: A 746 GLU cc_start: 0.8594 (tt0) cc_final: 0.8308 (tt0) REVERT: A 762 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: A 895 ARG cc_start: 0.6549 (mtp180) cc_final: 0.6156 (tpt170) REVERT: A 919 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7569 (ttm170) REVERT: A 925 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6689 (mtm180) REVERT: A 1108 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8735 (mt-10) REVERT: A 1194 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8646 (mp) outliers start: 32 outliers final: 21 residues processed: 125 average time/residue: 0.0934 time to fit residues: 17.3714 Evaluate side-chains 124 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A 595 HIS ** 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 = 0.3753 r_free = 0.3753 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.078042 restraints weight = 25934.391| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.54 r_work: 0.3003 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13127 Z= 0.147 Angle : 0.510 11.465 18351 Z= 0.276 Chirality : 0.039 0.290 2167 Planarity : 0.003 0.046 1912 Dihedral : 20.267 178.944 3150 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.53 % Allowed : 18.72 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.23), residues: 1332 helix: 1.13 (0.21), residues: 677 sheet: -0.88 (0.46), residues: 131 loop : -1.23 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A 491 TRP 0.013 0.001 TRP A1074 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (13127) covalent geometry : angle 0.51029 / 0.28 (18351) hydrogen bonds : bond 0.03871 / 2.61 ( 595) hydrogen bonds : angle 4.14622 / 2.98 ( 1633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8716 (mm) cc_final: 0.8511 (mp) REVERT: A 220 ARG cc_start: 0.8890 (ttp-170) cc_final: 0.8622 (ttp-170) REVERT: A 235 ASN cc_start: 0.8476 (m-40) cc_final: 0.7665 (t0) REVERT: A 307 ARG cc_start: 0.7868 (ptp-110) cc_final: 0.7538 (ptp90) REVERT: A 493 GLU cc_start: 0.8532 (pp20) cc_final: 0.8217 (pp20) REVERT: A 605 ASP cc_start: 0.8806 (t0) cc_final: 0.8229 (p0) REVERT: A 746 GLU cc_start: 0.8606 (tt0) cc_final: 0.8278 (tt0) REVERT: A 895 ARG cc_start: 0.6585 (mtp180) cc_final: 0.6202 (tpt170) REVERT: A 919 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7571 (ttm170) REVERT: A 947 ASP cc_start: 0.8548 (m-30) cc_final: 0.7960 (p0) REVERT: A 1108 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8763 (mt-10) REVERT: A 1194 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8703 (mp) outliers start: 33 outliers final: 24 residues processed: 129 average time/residue: 0.0959 time to fit residues: 18.5824 Evaluate side-chains 121 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 0.0370 chunk 44 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 143 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A 595 HIS ** 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 = 0.3767 r_free = 0.3767 target = 0.116189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079035 restraints weight = 25890.300| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.54 r_work: 0.3018 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13127 Z= 0.119 Angle : 0.499 11.225 18351 Z= 0.270 Chirality : 0.038 0.294 2167 Planarity : 0.003 0.045 1912 Dihedral : 20.150 179.470 3150 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.89 % Allowed : 19.14 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1332 helix: 1.21 (0.21), residues: 679 sheet: -0.84 (0.46), residues: 131 loop : -1.17 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.012 0.001 TYR A 155 PHE 0.011 0.001 PHE A 432 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (13127) covalent geometry : angle 0.49894 / 0.27 (18351) hydrogen bonds : bond 0.03682 / 2.49 ( 595) hydrogen bonds : angle 4.08032 / 2.94 ( 1633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 122 ILE cc_start: 0.8693 (mm) cc_final: 0.8479 (mp) REVERT: A 220 ARG cc_start: 0.8868 (ttp-170) cc_final: 0.8586 (ttp-170) REVERT: A 307 ARG cc_start: 0.7897 (ptp-110) cc_final: 0.7546 (ptp90) REVERT: A 493 GLU cc_start: 0.8504 (pp20) cc_final: 0.8192 (pp20) REVERT: A 605 ASP cc_start: 0.8819 (t0) cc_final: 0.8241 (p0) REVERT: A 746 GLU cc_start: 0.8549 (tt0) cc_final: 0.8217 (tt0) REVERT: A 895 ARG cc_start: 0.6602 (mtp180) cc_final: 0.6211 (tpt170) REVERT: A 919 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7569 (ttm170) REVERT: A 947 ASP cc_start: 0.8534 (m-30) cc_final: 0.7932 (p0) REVERT: A 1108 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8741 (mt-10) REVERT: A 1194 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8712 (mp) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.0909 time to fit residues: 16.0651 Evaluate side-chains 117 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 25 optimal weight: 0.2980 chunk 1 optimal weight: 0.2980 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 129 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.116650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079519 restraints weight = 25713.238| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.53 r_work: 0.3028 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13127 Z= 0.108 Angle : 0.491 11.212 18351 Z= 0.266 Chirality : 0.038 0.295 2167 Planarity : 0.003 0.045 1912 Dihedral : 20.079 179.805 3150 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.46 % Allowed : 20.32 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.23), residues: 1332 helix: 1.30 (0.21), residues: 679 sheet: -0.75 (0.46), residues: 131 loop : -1.12 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A 432 TRP 0.012 0.001 TRP A1074 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (13127) covalent geometry : angle 0.49053 / 0.27 (18351) hydrogen bonds : bond 0.03537 / 2.38 ( 595) hydrogen bonds : angle 4.04880 / 2.93 ( 1633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8876 (ttp-170) cc_final: 0.8595 (ttp-170) REVERT: A 307 ARG cc_start: 0.7908 (ptp-110) cc_final: 0.7538 (ptp90) REVERT: A 327 GLU cc_start: 0.7990 (pp20) cc_final: 0.7690 (pp20) REVERT: A 605 ASP cc_start: 0.8789 (t0) cc_final: 0.8230 (p0) REVERT: A 746 GLU cc_start: 0.8469 (tt0) cc_final: 0.8190 (tt0) REVERT: A 895 ARG cc_start: 0.6603 (mtp180) cc_final: 0.6210 (tpt170) REVERT: A 919 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7537 (ttm170) REVERT: A 947 ASP cc_start: 0.8533 (m-30) cc_final: 0.7928 (p0) REVERT: A 1108 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8753 (mt-10) REVERT: A 1194 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8733 (mp) outliers start: 23 outliers final: 20 residues processed: 115 average time/residue: 0.0948 time to fit residues: 15.9739 Evaluate side-chains 116 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A 497 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 = 0.3751 r_free = 0.3751 target = 0.115067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.077794 restraints weight = 25869.796| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.52 r_work: 0.2995 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13127 Z= 0.149 Angle : 0.516 10.894 18351 Z= 0.278 Chirality : 0.039 0.289 2167 Planarity : 0.003 0.047 1912 Dihedral : 20.060 178.878 3150 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.21 % Allowed : 19.36 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1332 helix: 1.31 (0.21), residues: 679 sheet: -0.69 (0.48), residues: 123 loop : -1.13 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.013 0.001 TYR A 155 PHE 0.013 0.001 PHE A 432 TRP 0.006 0.001 TRP A1074 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (13127) covalent geometry : angle 0.51636 / 0.28 (18351) hydrogen bonds : bond 0.03815 / 2.58 ( 595) hydrogen bonds : angle 4.04598 / 2.91 ( 1633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8894 (ttp-170) cc_final: 0.8600 (ttp-170) REVERT: A 605 ASP cc_start: 0.8768 (t0) cc_final: 0.8213 (p0) REVERT: A 746 GLU cc_start: 0.8571 (tt0) cc_final: 0.8234 (tt0) REVERT: A 895 ARG cc_start: 0.6570 (mtp180) cc_final: 0.6177 (tpt170) REVERT: A 919 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7560 (ttm170) REVERT: A 947 ASP cc_start: 0.8504 (m-30) cc_final: 0.7857 (p0) REVERT: A 1108 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 1269 ILE cc_start: 0.9163 (tt) cc_final: 0.8754 (mt) outliers start: 30 outliers final: 21 residues processed: 120 average time/residue: 0.1001 time to fit residues: 17.8731 Evaluate side-chains 116 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 133 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** 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 = 0.3734 r_free = 0.3734 target = 0.113920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.076486 restraints weight = 26066.458| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.51 r_work: 0.2969 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13127 Z= 0.187 Angle : 0.553 13.459 18351 Z= 0.295 Chirality : 0.040 0.287 2167 Planarity : 0.004 0.048 1912 Dihedral : 20.100 179.439 3150 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.57 % Allowed : 19.89 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1332 helix: 1.35 (0.21), residues: 674 sheet: -0.87 (0.47), residues: 126 loop : -1.08 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 215 TYR 0.013 0.001 TYR A 155 PHE 0.014 0.001 PHE A 432 TRP 0.016 0.001 TRP A1074 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (13127) covalent geometry : angle 0.55294 / 0.30 (18351) hydrogen bonds : bond 0.04034 / 2.70 ( 595) hydrogen bonds : angle 4.12005 / 2.98 ( 1633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8913 (ttp-170) cc_final: 0.8640 (ttp-170) REVERT: A 307 ARG cc_start: 0.7933 (ptp-110) cc_final: 0.7280 (ptp90) REVERT: A 605 ASP cc_start: 0.8784 (t0) cc_final: 0.8201 (p0) REVERT: A 746 GLU cc_start: 0.8595 (tt0) cc_final: 0.8259 (tt0) REVERT: A 895 ARG cc_start: 0.6579 (mtp180) cc_final: 0.6160 (tpt170) REVERT: A 919 ARG cc_start: 0.7988 (ttm170) cc_final: 0.7573 (ttm170) REVERT: A 947 ASP cc_start: 0.8516 (m-30) cc_final: 0.7854 (p0) REVERT: A 1108 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8795 (mt-10) outliers start: 24 outliers final: 20 residues processed: 111 average time/residue: 0.0997 time to fit residues: 16.5747 Evaluate side-chains 111 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 28 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 HIS A 281 GLN A 459 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.115470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078098 restraints weight = 25807.270| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.52 r_work: 0.3006 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13127 Z= 0.119 Angle : 0.505 12.718 18351 Z= 0.273 Chirality : 0.038 0.292 2167 Planarity : 0.003 0.045 1912 Dihedral : 20.040 179.067 3150 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.14 % Allowed : 20.21 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1332 helix: 1.44 (0.21), residues: 675 sheet: -0.82 (0.47), residues: 124 loop : -1.02 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.011 0.001 TYR A 155 PHE 0.013 0.001 PHE A 432 TRP 0.006 0.001 TRP A 464 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13127) covalent geometry : angle 0.50529 / 0.27 (18351) hydrogen bonds : bond 0.03593 / 2.42 ( 595) hydrogen bonds : angle 4.01840 / 2.92 ( 1633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2833.15 seconds wall clock time: 49 minutes 12.23 seconds (2952.23 seconds total)