Starting phenix.real_space_refine on Wed Mar 4 05:25:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mku_48338/03_2026/9mku_48338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mku_48338/03_2026/9mku_48338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mku_48338/03_2026/9mku_48338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mku_48338/03_2026/9mku_48338.map" model { file = "/net/cci-nas-00/data/ceres_data/9mku_48338/03_2026/9mku_48338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mku_48338/03_2026/9mku_48338.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 36 5.49 5 S 21 5.16 5 C 6766 2.51 5 N 1769 2.21 5 O 2143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10735 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 8, 'rna3p': 19} Chain: "C" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 9978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9978 Classifications: {'peptide': 1207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 1179} Chain breaks: 9 Time building chain proxies: 2.77, per 1000 atoms: 0.26 Number of scatterers: 10735 At special positions: 0 Unit cell: (98.04, 110.08, 135.02, 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 21 16.00 P 36 15.00 O 2143 8.00 N 1769 7.00 C 6766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 521.1 milliseconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 51.8% alpha, 9.9% beta 12 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 66 removed outlier: 3.587A pdb=" N ASP A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.944A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.594A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 121' Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.824A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.577A pdb=" N LYS A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.589A pdb=" N GLU A 265 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.996A pdb=" N ASN A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 344 through 362 removed outlier: 4.395A pdb=" N VAL A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.917A pdb=" N LEU A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.057A pdb=" N ILE A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.915A pdb=" N PHE A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.978A pdb=" N LEU A 515 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.594A pdb=" N GLN A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.742A pdb=" N CYS A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 removed outlier: 4.209A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 667 through 674 removed outlier: 3.555A pdb=" N PHE A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 694 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'A' and resid 732 through 736 removed outlier: 3.539A pdb=" N LYS A 735 " --> pdb=" O PRO A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 754 removed outlier: 3.633A pdb=" N PHE A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 781 removed outlier: 3.689A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 removed outlier: 4.249A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 870 through 875 removed outlier: 3.978A pdb=" N GLU A 875 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 907 Processing helix chain 'A' and resid 952 through 964 Processing helix chain 'A' and resid 977 through 1000 Processing helix chain 'A' and resid 1019 through 1036 Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1169 through 1181 Processing helix chain 'A' and resid 1191 through 1198 Processing helix chain 'A' and resid 1200 through 1215 removed outlier: 3.645A pdb=" N LEU A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1275 removed outlier: 3.508A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1296 removed outlier: 3.805A pdb=" N GLN A1296 " --> pdb=" O PHE A1292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.737A pdb=" N HIS A 881 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 829 " --> pdb=" O HIS A 881 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23 removed outlier: 4.618A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 631 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N ALA A 619 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N TYR A 659 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 623 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 655 " --> pdb=" O ILE A 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.731A pdb=" N LYS A 288 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA7, first strand: chain 'A' and resid 848 through 850 Processing sheet with id=AA8, first strand: chain 'A' and resid 935 through 940 removed outlier: 6.839A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL A1004 " --> pdb=" O HIS A 912 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 914 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N GLU A1006 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N ILE A 916 " --> pdb=" O GLU A1006 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1114 through 1118 Processing sheet with id=AB1, first strand: chain 'A' and resid 1150 through 1153 Processing sheet with id=AB2, first strand: chain 'A' and resid 1218 through 1219 450 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3166 1.34 - 1.45: 1908 1.45 - 1.57: 5839 1.57 - 1.69: 70 1.69 - 1.81: 33 Bond restraints: 11016 Sorted by residual: bond pdb=" N GLU A1189 " pdb=" CA GLU A1189 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.88e+00 bond pdb=" N CYS A1190 " pdb=" CA CYS A1190 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.76e+00 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.18e-02 7.18e+03 6.14e+00 bond pdb=" N ILE A1191 " pdb=" CA ILE A1191 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.72e+00 bond pdb=" N ILE A 425 " pdb=" CA ILE A 425 " ideal model delta sigma weight residual 1.461 1.488 -0.027 1.17e-02 7.31e+03 5.37e+00 ... (remaining 11011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 14883 2.76 - 5.51: 71 5.51 - 8.27: 4 8.27 - 11.03: 1 11.03 - 13.78: 1 Bond angle restraints: 14960 Sorted by residual: angle pdb=" N GLN A 424 " pdb=" CA GLN A 424 " pdb=" C GLN A 424 " ideal model delta sigma weight residual 112.45 98.67 13.78 1.39e+00 5.18e-01 9.83e+01 angle pdb=" N GLN A 423 " pdb=" CA GLN A 423 " pdb=" C GLN A 423 " ideal model delta sigma weight residual 111.28 119.54 -8.26 1.09e+00 8.42e-01 5.74e+01 angle pdb=" C GLN A 423 " pdb=" CA GLN A 423 " pdb=" CB GLN A 423 " ideal model delta sigma weight residual 110.79 100.78 10.01 1.66e+00 3.63e-01 3.64e+01 angle pdb=" N GLU A 461 " pdb=" CA GLU A 461 " pdb=" C GLU A 461 " ideal model delta sigma weight residual 111.28 107.35 3.93 1.09e+00 8.42e-01 1.30e+01 angle pdb=" C ILE A 575 " pdb=" N VAL A 576 " pdb=" CA VAL A 576 " ideal model delta sigma weight residual 120.24 122.43 -2.19 6.30e-01 2.52e+00 1.21e+01 ... (remaining 14955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5995 17.87 - 35.75: 501 35.75 - 53.62: 121 53.62 - 71.49: 71 71.49 - 89.36: 10 Dihedral angle restraints: 6698 sinusoidal: 3116 harmonic: 3582 Sorted by residual: dihedral pdb=" CA LYS A 973 " pdb=" C LYS A 973 " pdb=" N ILE A 974 " pdb=" CA ILE A 974 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 205 " pdb=" CB ASP A 205 " pdb=" CG ASP A 205 " pdb=" OD1 ASP A 205 " ideal model delta sinusoidal sigma weight residual -30.00 -86.98 56.98 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU A 829 " pdb=" CG GLU A 829 " pdb=" CD GLU A 829 " pdb=" OE1 GLU A 829 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 6695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1427 0.059 - 0.118: 183 0.118 - 0.177: 15 0.177 - 0.236: 4 0.236 - 0.295: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CA GLN A 424 " pdb=" N GLN A 424 " pdb=" C GLN A 424 " pdb=" CB GLN A 424 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ILE A1191 " pdb=" N ILE A1191 " pdb=" C ILE A1191 " pdb=" CB ILE A1191 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE A 425 " pdb=" N ILE A 425 " pdb=" C ILE A 425 " pdb=" CB ILE A 425 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1627 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1188 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLY A1188 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY A1188 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A1189 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 987 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLN A 987 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 987 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 988 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 986 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C SER A 986 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 986 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 987 " 0.011 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 981 2.74 - 3.28: 11591 3.28 - 3.82: 18608 3.82 - 4.36: 21694 4.36 - 4.90: 33838 Nonbonded interactions: 86712 Sorted by model distance: nonbonded pdb=" O PHE A1147 " pdb=" NH1 ARG A1150 " model vdw 2.201 3.120 nonbonded pdb=" NE2 GLN A1106 " pdb=" O CYS A1196 " model vdw 2.211 3.120 nonbonded pdb=" O GLY A 286 " pdb=" NZ LYS A 296 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR A1181 " pdb=" OD2 ASP A1200 " model vdw 2.256 3.040 nonbonded pdb=" ND2 ASN A 156 " pdb=" OD1 ASP A 158 " model vdw 2.263 3.120 ... (remaining 86707 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11016 Z= 0.154 Angle : 0.547 13.782 14960 Z= 0.330 Chirality : 0.041 0.295 1630 Planarity : 0.003 0.035 1786 Dihedral : 15.485 89.364 4378 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 0.27 % Allowed : 1.00 % Favored : 98.73 % 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 (0.24), residues: 1187 helix: 0.62 (0.22), residues: 555 sheet: -0.88 (0.48), residues: 122 loop : -0.79 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 583 TYR 0.015 0.001 TYR A 79 PHE 0.028 0.001 PHE A 720 TRP 0.007 0.001 TRP A1142 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00271 (11016) covalent geometry : angle 0.54730 (14960) hydrogen bonds : bond 0.16616 ( 476) hydrogen bonds : angle 6.03963 ( 1342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9214 (m-80) cc_final: 0.8293 (m-80) REVERT: A 46 ASP cc_start: 0.9462 (m-30) cc_final: 0.9185 (t0) REVERT: A 65 ILE cc_start: 0.9421 (tp) cc_final: 0.9187 (pt) REVERT: A 138 LEU cc_start: 0.9304 (mt) cc_final: 0.9030 (mt) REVERT: A 175 TRP cc_start: 0.8257 (m100) cc_final: 0.6790 (m-10) REVERT: A 312 ASN cc_start: 0.9164 (t0) cc_final: 0.8915 (m-40) REVERT: A 366 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9034 (pm20) REVERT: A 378 PHE cc_start: 0.9331 (m-10) cc_final: 0.8937 (m-80) REVERT: A 389 SER cc_start: 0.9028 (p) cc_final: 0.8460 (p) REVERT: A 487 MET cc_start: 0.9362 (ptt) cc_final: 0.8682 (tpt) REVERT: A 536 LEU cc_start: 0.9736 (tp) cc_final: 0.9468 (mt) REVERT: A 595 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8505 (mtpp) REVERT: A 647 LYS cc_start: 0.9485 (tppt) cc_final: 0.9282 (mmmt) REVERT: A 659 TYR cc_start: 0.9276 (t80) cc_final: 0.8822 (t80) REVERT: A 668 MET cc_start: 0.9537 (mmp) cc_final: 0.9282 (mmm) REVERT: A 746 ARG cc_start: 0.9204 (ttm170) cc_final: 0.8978 (mtm-85) REVERT: A 811 LEU cc_start: 0.9175 (mt) cc_final: 0.8920 (mt) REVERT: A 868 ILE cc_start: 0.9152 (mt) cc_final: 0.8901 (mm) REVERT: A 949 MET cc_start: 0.5977 (pmm) cc_final: 0.5775 (pmm) REVERT: A 971 TRP cc_start: 0.9446 (t60) cc_final: 0.9091 (t60) REVERT: A 1026 LYS cc_start: 0.9479 (tppt) cc_final: 0.9249 (tppt) REVERT: A 1067 MET cc_start: 0.8568 (mtm) cc_final: 0.8214 (mtt) REVERT: A 1100 GLU cc_start: 0.9715 (mt-10) cc_final: 0.9445 (mm-30) REVERT: A 1218 ARG cc_start: 0.8957 (ttm170) cc_final: 0.8133 (tpt170) REVERT: A 1250 MET cc_start: 0.8475 (mmm) cc_final: 0.7711 (mmm) outliers start: 3 outliers final: 1 residues processed: 334 average time/residue: 0.1367 time to fit residues: 60.0650 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1190 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.0470 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 188 ASN A 214 ASN A 274 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 508 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.110873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.090341 restraints weight = 54127.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.092185 restraints weight = 42209.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.093408 restraints weight = 34451.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.094386 restraints weight = 29720.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095065 restraints weight = 26507.791| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11016 Z= 0.155 Angle : 0.663 12.008 14960 Z= 0.347 Chirality : 0.042 0.202 1630 Planarity : 0.004 0.048 1786 Dihedral : 13.110 81.239 1798 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 2.91 % Allowed : 11.92 % Favored : 85.17 % 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 are not related in a simple way. whole: -0.13 (0.24), residues: 1187 helix: 0.70 (0.21), residues: 564 sheet: -0.75 (0.50), residues: 116 loop : -0.73 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1155 TYR 0.024 0.002 TYR A 807 PHE 0.024 0.002 PHE A 720 TRP 0.020 0.002 TRP A 734 HIS 0.005 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00334 (11016) covalent geometry : angle 0.66298 (14960) hydrogen bonds : bond 0.05400 ( 476) hydrogen bonds : angle 5.02693 ( 1342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9136 (m-80) cc_final: 0.8218 (m-80) REVERT: A 46 ASP cc_start: 0.9385 (m-30) cc_final: 0.9141 (t70) REVERT: A 65 ILE cc_start: 0.9414 (tp) cc_final: 0.9129 (pt) REVERT: A 138 LEU cc_start: 0.9258 (mt) cc_final: 0.9055 (mt) REVERT: A 366 GLU cc_start: 0.9346 (mm-30) cc_final: 0.8993 (pm20) REVERT: A 400 THR cc_start: 0.9613 (p) cc_final: 0.9314 (t) REVERT: A 595 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8573 (mtpp) REVERT: A 647 LYS cc_start: 0.9501 (tppt) cc_final: 0.9264 (mmmt) REVERT: A 659 TYR cc_start: 0.9214 (t80) cc_final: 0.8709 (t80) REVERT: A 668 MET cc_start: 0.9545 (mmp) cc_final: 0.9204 (mmm) REVERT: A 746 ARG cc_start: 0.9243 (ttm170) cc_final: 0.8846 (ptp-110) REVERT: A 807 TYR cc_start: 0.9052 (m-80) cc_final: 0.8836 (m-80) REVERT: A 811 LEU cc_start: 0.9092 (mt) cc_final: 0.8833 (mt) REVERT: A 868 ILE cc_start: 0.9071 (mt) cc_final: 0.8856 (mm) REVERT: A 870 ASP cc_start: 0.8949 (m-30) cc_final: 0.8593 (t0) REVERT: A 949 MET cc_start: 0.6238 (pmm) cc_final: 0.6002 (pmm) REVERT: A 971 TRP cc_start: 0.9419 (t60) cc_final: 0.9076 (t60) REVERT: A 976 ASN cc_start: 0.8996 (m-40) cc_final: 0.8048 (t0) REVERT: A 1007 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6982 (m-30) REVERT: A 1026 LYS cc_start: 0.9412 (tppt) cc_final: 0.9143 (tppt) REVERT: A 1030 MET cc_start: 0.9489 (mmp) cc_final: 0.8693 (mmp) REVERT: A 1100 GLU cc_start: 0.9730 (mt-10) cc_final: 0.9394 (mm-30) REVERT: A 1250 MET cc_start: 0.8391 (mmm) cc_final: 0.7882 (mmm) outliers start: 32 outliers final: 18 residues processed: 248 average time/residue: 0.1164 time to fit residues: 39.2344 Evaluate side-chains 217 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 538 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.110002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.090419 restraints weight = 55483.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092152 restraints weight = 42558.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.093504 restraints weight = 34653.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094339 restraints weight = 29492.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.094780 restraints weight = 26496.892| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11016 Z= 0.145 Angle : 0.638 11.306 14960 Z= 0.333 Chirality : 0.040 0.174 1630 Planarity : 0.004 0.067 1786 Dihedral : 13.055 78.971 1797 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 3.18 % Allowed : 15.92 % Favored : 80.89 % 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: -0.28 (0.24), residues: 1187 helix: 0.54 (0.21), residues: 566 sheet: -0.54 (0.52), residues: 106 loop : -0.84 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 43 TYR 0.018 0.002 TYR A1291 PHE 0.027 0.002 PHE A 880 TRP 0.027 0.003 TRP A 175 HIS 0.005 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00308 (11016) covalent geometry : angle 0.63754 (14960) hydrogen bonds : bond 0.04679 ( 476) hydrogen bonds : angle 4.87296 ( 1342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9142 (m-80) cc_final: 0.8244 (m-80) REVERT: A 65 ILE cc_start: 0.9444 (tp) cc_final: 0.9141 (pt) REVERT: A 138 LEU cc_start: 0.9267 (mt) cc_final: 0.9058 (mt) REVERT: A 366 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9127 (pm20) REVERT: A 392 TYR cc_start: 0.9505 (m-80) cc_final: 0.8970 (m-80) REVERT: A 498 ASN cc_start: 0.9525 (t0) cc_final: 0.9211 (m-40) REVERT: A 595 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8731 (mtpp) REVERT: A 643 ASP cc_start: 0.9251 (p0) cc_final: 0.8813 (p0) REVERT: A 647 LYS cc_start: 0.9526 (tppt) cc_final: 0.9321 (mmmt) REVERT: A 659 TYR cc_start: 0.9268 (t80) cc_final: 0.8742 (t80) REVERT: A 668 MET cc_start: 0.9463 (mmp) cc_final: 0.9220 (mmm) REVERT: A 746 ARG cc_start: 0.9251 (ttm170) cc_final: 0.8865 (ptp-110) REVERT: A 807 TYR cc_start: 0.9065 (m-80) cc_final: 0.8830 (m-80) REVERT: A 811 LEU cc_start: 0.9067 (mt) cc_final: 0.8809 (mt) REVERT: A 868 ILE cc_start: 0.9022 (mt) cc_final: 0.8754 (mm) REVERT: A 870 ASP cc_start: 0.8931 (m-30) cc_final: 0.8725 (m-30) REVERT: A 949 MET cc_start: 0.6234 (pmm) cc_final: 0.5988 (pmm) REVERT: A 971 TRP cc_start: 0.9413 (t60) cc_final: 0.9070 (t60) REVERT: A 976 ASN cc_start: 0.9089 (m-40) cc_final: 0.8065 (t0) REVERT: A 1007 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: A 1008 LEU cc_start: 0.4870 (mt) cc_final: 0.4409 (mt) REVERT: A 1100 GLU cc_start: 0.9729 (mt-10) cc_final: 0.9390 (mm-30) REVERT: A 1250 MET cc_start: 0.8410 (mmm) cc_final: 0.7927 (mmm) outliers start: 35 outliers final: 23 residues processed: 234 average time/residue: 0.1087 time to fit residues: 35.0703 Evaluate side-chains 219 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 0.0050 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 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 = 0.4007 r_free = 0.4007 target = 0.109014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.089143 restraints weight = 55645.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.090930 restraints weight = 42704.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.092274 restraints weight = 34474.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093192 restraints weight = 29314.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.093840 restraints weight = 26118.173| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11016 Z= 0.135 Angle : 0.629 11.346 14960 Z= 0.327 Chirality : 0.040 0.239 1630 Planarity : 0.004 0.051 1786 Dihedral : 13.032 80.914 1797 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 3.46 % Allowed : 17.29 % Favored : 79.25 % 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: -0.32 (0.24), residues: 1187 helix: 0.56 (0.21), residues: 564 sheet: -0.47 (0.53), residues: 106 loop : -0.96 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 43 TYR 0.024 0.002 TYR A 984 PHE 0.030 0.002 PHE A 880 TRP 0.034 0.003 TRP A 175 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00278 (11016) covalent geometry : angle 0.62889 (14960) hydrogen bonds : bond 0.04366 ( 476) hydrogen bonds : angle 4.74907 ( 1342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9067 (m-80) cc_final: 0.8211 (m-80) REVERT: A 65 ILE cc_start: 0.9479 (tp) cc_final: 0.9142 (pt) REVERT: A 118 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8656 (mmmt) REVERT: A 138 LEU cc_start: 0.9272 (mt) cc_final: 0.9071 (mt) REVERT: A 234 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8890 (pt) REVERT: A 366 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9161 (pm20) REVERT: A 498 ASN cc_start: 0.9517 (t0) cc_final: 0.9191 (m-40) REVERT: A 538 HIS cc_start: 0.9561 (m-70) cc_final: 0.9199 (m-70) REVERT: A 595 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8732 (mtpp) REVERT: A 643 ASP cc_start: 0.9267 (p0) cc_final: 0.8827 (p0) REVERT: A 659 TYR cc_start: 0.9204 (t80) cc_final: 0.8703 (t80) REVERT: A 668 MET cc_start: 0.9453 (mmp) cc_final: 0.9194 (mmm) REVERT: A 736 ASP cc_start: 0.9409 (m-30) cc_final: 0.9206 (p0) REVERT: A 746 ARG cc_start: 0.9233 (ttm170) cc_final: 0.8873 (ptp-110) REVERT: A 807 TYR cc_start: 0.9016 (m-80) cc_final: 0.8773 (m-80) REVERT: A 811 LEU cc_start: 0.9042 (mt) cc_final: 0.8787 (mt) REVERT: A 868 ILE cc_start: 0.8949 (mt) cc_final: 0.8690 (mm) REVERT: A 870 ASP cc_start: 0.8830 (m-30) cc_final: 0.8608 (m-30) REVERT: A 971 TRP cc_start: 0.9379 (t60) cc_final: 0.9047 (t60) REVERT: A 976 ASN cc_start: 0.9177 (m-40) cc_final: 0.8164 (t0) REVERT: A 1007 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: A 1008 LEU cc_start: 0.5407 (mt) cc_final: 0.4559 (mt) REVERT: A 1100 GLU cc_start: 0.9711 (mt-10) cc_final: 0.9373 (mm-30) REVERT: A 1250 MET cc_start: 0.8389 (mmm) cc_final: 0.7873 (mmm) REVERT: A 1260 TYR cc_start: 0.9337 (t80) cc_final: 0.9081 (t80) REVERT: A 1264 LEU cc_start: 0.8816 (tp) cc_final: 0.8169 (mt) outliers start: 38 outliers final: 27 residues processed: 223 average time/residue: 0.1043 time to fit residues: 32.4007 Evaluate side-chains 214 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 78 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.114691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.094249 restraints weight = 52478.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.096498 restraints weight = 36262.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.098052 restraints weight = 27743.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.098998 restraints weight = 22823.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.099922 restraints weight = 20032.642| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11016 Z= 0.125 Angle : 0.644 14.678 14960 Z= 0.328 Chirality : 0.041 0.275 1630 Planarity : 0.003 0.053 1786 Dihedral : 12.974 80.509 1797 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 3.09 % Allowed : 18.56 % Favored : 78.34 % 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 (0.24), residues: 1187 helix: 0.66 (0.22), residues: 556 sheet: -0.50 (0.51), residues: 113 loop : -0.90 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.020 0.001 TYR A 201 PHE 0.030 0.002 PHE A 880 TRP 0.023 0.003 TRP A 175 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00259 (11016) covalent geometry : angle 0.64353 (14960) hydrogen bonds : bond 0.04179 ( 476) hydrogen bonds : angle 4.58501 ( 1342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9175 (m-80) cc_final: 0.8314 (m-80) REVERT: A 65 ILE cc_start: 0.9401 (tp) cc_final: 0.9137 (pt) REVERT: A 166 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9088 (mt) REVERT: A 366 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9175 (pm20) REVERT: A 451 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9172 (pt) REVERT: A 491 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8838 (mm-30) REVERT: A 498 ASN cc_start: 0.9497 (t0) cc_final: 0.9168 (m-40) REVERT: A 538 HIS cc_start: 0.9573 (m-70) cc_final: 0.9176 (m-70) REVERT: A 595 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8752 (mtpp) REVERT: A 599 ASN cc_start: 0.6984 (t0) cc_final: 0.6496 (t0) REVERT: A 602 ASN cc_start: 0.7783 (t0) cc_final: 0.7468 (t0) REVERT: A 659 TYR cc_start: 0.9185 (t80) cc_final: 0.8694 (t80) REVERT: A 668 MET cc_start: 0.9441 (mmp) cc_final: 0.9166 (mmm) REVERT: A 746 ARG cc_start: 0.9199 (ttm170) cc_final: 0.8833 (ptp-110) REVERT: A 811 LEU cc_start: 0.9079 (mt) cc_final: 0.8825 (mt) REVERT: A 868 ILE cc_start: 0.9048 (mt) cc_final: 0.8797 (mm) REVERT: A 870 ASP cc_start: 0.8974 (m-30) cc_final: 0.8755 (m-30) REVERT: A 971 TRP cc_start: 0.9332 (t60) cc_final: 0.9011 (t60) REVERT: A 976 ASN cc_start: 0.9144 (m-40) cc_final: 0.8156 (t0) REVERT: A 1007 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: A 1008 LEU cc_start: 0.5483 (mt) cc_final: 0.4778 (mt) REVERT: A 1100 GLU cc_start: 0.9698 (mt-10) cc_final: 0.9362 (mm-30) REVERT: A 1250 MET cc_start: 0.8367 (mmm) cc_final: 0.7922 (mmm) REVERT: A 1260 TYR cc_start: 0.9338 (t80) cc_final: 0.9065 (t80) outliers start: 34 outliers final: 21 residues processed: 230 average time/residue: 0.1072 time to fit residues: 34.2465 Evaluate side-chains 207 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 85 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 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 = 0.4180 r_free = 0.4180 target = 0.115002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.094351 restraints weight = 51434.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.096593 restraints weight = 35533.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.097930 restraints weight = 27204.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.099238 restraints weight = 22784.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.100075 restraints weight = 19470.515| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11016 Z= 0.121 Angle : 0.628 13.674 14960 Z= 0.321 Chirality : 0.041 0.192 1630 Planarity : 0.003 0.054 1786 Dihedral : 12.895 80.263 1797 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 3.09 % Allowed : 19.75 % Favored : 77.16 % 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 (0.24), residues: 1187 helix: 0.71 (0.21), residues: 556 sheet: -0.67 (0.49), residues: 120 loop : -0.93 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 583 TYR 0.034 0.001 TYR A 807 PHE 0.031 0.002 PHE A 880 TRP 0.025 0.003 TRP A 175 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00253 (11016) covalent geometry : angle 0.62787 (14960) hydrogen bonds : bond 0.04071 ( 476) hydrogen bonds : angle 4.47705 ( 1342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9144 (m-80) cc_final: 0.8298 (m-80) REVERT: A 65 ILE cc_start: 0.9402 (tp) cc_final: 0.9106 (pt) REVERT: A 166 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9123 (mt) REVERT: A 366 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9193 (pm20) REVERT: A 451 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9167 (pt) REVERT: A 494 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6964 (pm20) REVERT: A 498 ASN cc_start: 0.9500 (t0) cc_final: 0.9149 (m-40) REVERT: A 595 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8748 (mtpp) REVERT: A 602 ASN cc_start: 0.7844 (t0) cc_final: 0.7621 (t0) REVERT: A 659 TYR cc_start: 0.9233 (t80) cc_final: 0.8794 (t80) REVERT: A 668 MET cc_start: 0.9431 (mmp) cc_final: 0.9156 (mmm) REVERT: A 811 LEU cc_start: 0.9051 (mt) cc_final: 0.8784 (mt) REVERT: A 868 ILE cc_start: 0.9023 (mt) cc_final: 0.8771 (mm) REVERT: A 870 ASP cc_start: 0.8919 (m-30) cc_final: 0.8683 (m-30) REVERT: A 971 TRP cc_start: 0.9311 (t60) cc_final: 0.8994 (t60) REVERT: A 975 ASN cc_start: 0.9114 (t0) cc_final: 0.8468 (m-40) REVERT: A 976 ASN cc_start: 0.9107 (m-40) cc_final: 0.8061 (t0) REVERT: A 991 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8943 (tm-30) REVERT: A 1007 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: A 1008 LEU cc_start: 0.5583 (mt) cc_final: 0.4938 (mt) REVERT: A 1100 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9343 (mm-30) REVERT: A 1250 MET cc_start: 0.8391 (mmm) cc_final: 0.7949 (mmm) outliers start: 34 outliers final: 22 residues processed: 210 average time/residue: 0.1127 time to fit residues: 32.8162 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 98 optimal weight: 0.0570 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 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 = 0.4180 r_free = 0.4180 target = 0.115116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.094502 restraints weight = 51702.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.096773 restraints weight = 35898.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.098371 restraints weight = 27410.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099346 restraints weight = 22417.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.100232 restraints weight = 19582.293| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11016 Z= 0.122 Angle : 0.648 13.976 14960 Z= 0.330 Chirality : 0.041 0.342 1630 Planarity : 0.004 0.057 1786 Dihedral : 12.900 80.099 1797 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 2.73 % Allowed : 20.20 % Favored : 77.07 % 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 are not related in a simple way. whole: -0.22 (0.24), residues: 1187 helix: 0.71 (0.22), residues: 559 sheet: -0.35 (0.51), residues: 113 loop : -1.00 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 202 TYR 0.037 0.001 TYR A 807 PHE 0.030 0.001 PHE A 880 TRP 0.031 0.003 TRP A 609 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00256 (11016) covalent geometry : angle 0.64753 (14960) hydrogen bonds : bond 0.03975 ( 476) hydrogen bonds : angle 4.51151 ( 1342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9132 (m-80) cc_final: 0.8294 (m-80) REVERT: A 32 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8248 (mmtt) REVERT: A 65 ILE cc_start: 0.9406 (tp) cc_final: 0.9152 (pt) REVERT: A 118 LYS cc_start: 0.8837 (tptt) cc_final: 0.8625 (mmmt) REVERT: A 166 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9093 (mt) REVERT: A 366 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9135 (pm20) REVERT: A 451 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9170 (pt) REVERT: A 494 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: A 498 ASN cc_start: 0.9495 (t0) cc_final: 0.9147 (m-40) REVERT: A 595 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8756 (mtpp) REVERT: A 602 ASN cc_start: 0.7963 (t0) cc_final: 0.7459 (t0) REVERT: A 659 TYR cc_start: 0.9158 (t80) cc_final: 0.8801 (t80) REVERT: A 668 MET cc_start: 0.9429 (mmp) cc_final: 0.9159 (mmm) REVERT: A 746 ARG cc_start: 0.9187 (ttm170) cc_final: 0.8848 (ptp-110) REVERT: A 811 LEU cc_start: 0.9053 (mt) cc_final: 0.8788 (mt) REVERT: A 868 ILE cc_start: 0.9007 (mt) cc_final: 0.8732 (mm) REVERT: A 870 ASP cc_start: 0.8871 (m-30) cc_final: 0.8624 (m-30) REVERT: A 941 PHE cc_start: 0.8406 (m-80) cc_final: 0.7965 (m-80) REVERT: A 965 ASP cc_start: 0.8697 (t70) cc_final: 0.8151 (m-30) REVERT: A 976 ASN cc_start: 0.9090 (m-40) cc_final: 0.8596 (t0) REVERT: A 991 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8974 (tm-30) REVERT: A 1100 GLU cc_start: 0.9675 (mt-10) cc_final: 0.9344 (mm-30) REVERT: A 1239 ASN cc_start: 0.8587 (t0) cc_final: 0.7929 (m110) REVERT: A 1250 MET cc_start: 0.8399 (mmm) cc_final: 0.7923 (mmm) outliers start: 30 outliers final: 24 residues processed: 213 average time/residue: 0.1108 time to fit residues: 32.8357 Evaluate side-chains 210 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A1070 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.089738 restraints weight = 54258.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.091579 restraints weight = 40718.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.092798 restraints weight = 32877.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.093688 restraints weight = 28287.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.094356 restraints weight = 25210.385| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11016 Z= 0.137 Angle : 0.681 15.001 14960 Z= 0.347 Chirality : 0.041 0.290 1630 Planarity : 0.003 0.058 1786 Dihedral : 12.960 78.444 1797 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 2.73 % Allowed : 20.84 % Favored : 76.43 % 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: -0.38 (0.24), residues: 1187 helix: 0.61 (0.21), residues: 564 sheet: -0.93 (0.48), residues: 125 loop : -1.00 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 43 TYR 0.039 0.002 TYR A 807 PHE 0.033 0.002 PHE A 880 TRP 0.036 0.003 TRP A 609 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00293 (11016) covalent geometry : angle 0.68083 (14960) hydrogen bonds : bond 0.04067 ( 476) hydrogen bonds : angle 4.57003 ( 1342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8965 (m-80) cc_final: 0.8193 (m-80) REVERT: A 32 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8232 (mmtt) REVERT: A 65 ILE cc_start: 0.9412 (tp) cc_final: 0.9168 (pt) REVERT: A 118 LYS cc_start: 0.8904 (tptt) cc_final: 0.8676 (tptt) REVERT: A 166 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9089 (mt) REVERT: A 275 GLN cc_start: 0.8247 (mm110) cc_final: 0.8027 (mm-40) REVERT: A 366 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9136 (pm20) REVERT: A 451 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9199 (pt) REVERT: A 494 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: A 498 ASN cc_start: 0.9502 (t0) cc_final: 0.9161 (m-40) REVERT: A 538 HIS cc_start: 0.9553 (m90) cc_final: 0.9183 (m-70) REVERT: A 595 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8680 (mtpp) REVERT: A 602 ASN cc_start: 0.7993 (t0) cc_final: 0.7513 (t0) REVERT: A 659 TYR cc_start: 0.9098 (t80) cc_final: 0.8634 (t80) REVERT: A 668 MET cc_start: 0.9435 (mmp) cc_final: 0.9157 (mmm) REVERT: A 720 PHE cc_start: 0.9286 (t80) cc_final: 0.8946 (t80) REVERT: A 746 ARG cc_start: 0.9218 (ttm170) cc_final: 0.8869 (ptp-110) REVERT: A 811 LEU cc_start: 0.9038 (mt) cc_final: 0.8760 (mt) REVERT: A 868 ILE cc_start: 0.8903 (mt) cc_final: 0.8663 (mm) REVERT: A 870 ASP cc_start: 0.8608 (m-30) cc_final: 0.8345 (m-30) REVERT: A 941 PHE cc_start: 0.8359 (m-80) cc_final: 0.7946 (m-80) REVERT: A 965 ASP cc_start: 0.8613 (t70) cc_final: 0.8071 (m-30) REVERT: A 975 ASN cc_start: 0.9464 (t0) cc_final: 0.9193 (m110) REVERT: A 976 ASN cc_start: 0.9199 (m-40) cc_final: 0.8305 (t0) REVERT: A 991 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8893 (tm-30) REVERT: A 1100 GLU cc_start: 0.9667 (mt-10) cc_final: 0.9333 (mm-30) REVERT: A 1239 ASN cc_start: 0.8591 (t0) cc_final: 0.7942 (m110) REVERT: A 1250 MET cc_start: 0.8452 (mmm) cc_final: 0.7924 (mmm) outliers start: 30 outliers final: 24 residues processed: 201 average time/residue: 0.1010 time to fit residues: 29.2381 Evaluate side-chains 205 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 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 = 0.3989 r_free = 0.3989 target = 0.107830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.088821 restraints weight = 55382.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.090620 restraints weight = 41689.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.091809 restraints weight = 33747.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.092675 restraints weight = 29005.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.093328 restraints weight = 25936.668| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11016 Z= 0.147 Angle : 0.687 14.227 14960 Z= 0.352 Chirality : 0.041 0.257 1630 Planarity : 0.003 0.061 1786 Dihedral : 13.088 77.137 1797 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.89 % Favored : 95.03 % Rotamer: Outliers : 3.00 % Allowed : 20.93 % Favored : 76.07 % 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 are not related in a simple way. whole: -0.43 (0.24), residues: 1187 helix: 0.56 (0.21), residues: 564 sheet: -1.06 (0.48), residues: 121 loop : -0.98 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.041 0.002 TYR A 807 PHE 0.034 0.002 PHE A 880 TRP 0.036 0.003 TRP A 609 HIS 0.003 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00313 (11016) covalent geometry : angle 0.68678 (14960) hydrogen bonds : bond 0.04142 ( 476) hydrogen bonds : angle 4.62486 ( 1342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9044 (m-80) cc_final: 0.8233 (m-80) REVERT: A 32 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8253 (mmtt) REVERT: A 65 ILE cc_start: 0.9438 (tp) cc_final: 0.9197 (pt) REVERT: A 118 LYS cc_start: 0.8969 (tptt) cc_final: 0.8749 (tptt) REVERT: A 166 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9081 (mt) REVERT: A 366 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9106 (pm20) REVERT: A 392 TYR cc_start: 0.9602 (m-80) cc_final: 0.8897 (m-10) REVERT: A 451 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9162 (pt) REVERT: A 494 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: A 498 ASN cc_start: 0.9503 (t0) cc_final: 0.9174 (m-40) REVERT: A 538 HIS cc_start: 0.9557 (m90) cc_final: 0.9114 (m170) REVERT: A 602 ASN cc_start: 0.8017 (t0) cc_final: 0.7495 (t0) REVERT: A 659 TYR cc_start: 0.9131 (t80) cc_final: 0.8791 (t80) REVERT: A 668 MET cc_start: 0.9444 (mmp) cc_final: 0.9169 (mmm) REVERT: A 720 PHE cc_start: 0.9282 (t80) cc_final: 0.8962 (t80) REVERT: A 746 ARG cc_start: 0.9233 (ttm170) cc_final: 0.8903 (ptp-170) REVERT: A 811 LEU cc_start: 0.9086 (mt) cc_final: 0.8811 (mt) REVERT: A 868 ILE cc_start: 0.8968 (mt) cc_final: 0.8728 (mm) REVERT: A 870 ASP cc_start: 0.8742 (m-30) cc_final: 0.8469 (m-30) REVERT: A 949 MET cc_start: 0.6898 (pmm) cc_final: 0.6481 (pmm) REVERT: A 964 ARG cc_start: 0.6691 (mmt180) cc_final: 0.5111 (mmt180) REVERT: A 965 ASP cc_start: 0.8594 (t70) cc_final: 0.8146 (m-30) REVERT: A 1100 GLU cc_start: 0.9672 (mt-10) cc_final: 0.9333 (mm-30) REVERT: A 1250 MET cc_start: 0.8511 (mmm) cc_final: 0.7934 (mmm) outliers start: 33 outliers final: 28 residues processed: 202 average time/residue: 0.1004 time to fit residues: 28.9740 Evaluate side-chains 207 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 971 TRP Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 72 optimal weight: 0.0370 chunk 112 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.115051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.094342 restraints weight = 52190.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.096550 restraints weight = 36349.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.098094 restraints weight = 28088.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.099178 restraints weight = 23075.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.099917 restraints weight = 19987.769| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11016 Z= 0.126 Angle : 0.710 14.151 14960 Z= 0.362 Chirality : 0.042 0.262 1630 Planarity : 0.003 0.059 1786 Dihedral : 13.056 77.687 1797 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 3.00 % Allowed : 20.93 % Favored : 76.07 % 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 are not related in a simple way. whole: -0.39 (0.24), residues: 1187 helix: 0.59 (0.22), residues: 565 sheet: -0.72 (0.49), residues: 114 loop : -1.04 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.043 0.002 TYR A 807 PHE 0.034 0.002 PHE A 880 TRP 0.039 0.003 TRP A 609 HIS 0.004 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00263 (11016) covalent geometry : angle 0.71030 (14960) hydrogen bonds : bond 0.04016 ( 476) hydrogen bonds : angle 4.55364 ( 1342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9194 (m-80) cc_final: 0.8334 (m-80) REVERT: A 65 ILE cc_start: 0.9449 (tp) cc_final: 0.9199 (pt) REVERT: A 118 LYS cc_start: 0.8968 (tptt) cc_final: 0.8700 (tptt) REVERT: A 166 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9105 (mt) REVERT: A 275 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8203 (mm-40) REVERT: A 366 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9114 (pm20) REVERT: A 392 TYR cc_start: 0.9580 (m-80) cc_final: 0.8831 (m-10) REVERT: A 451 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9192 (pt) REVERT: A 494 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: A 498 ASN cc_start: 0.9501 (t0) cc_final: 0.9161 (m-40) REVERT: A 538 HIS cc_start: 0.9548 (m90) cc_final: 0.9112 (m170) REVERT: A 659 TYR cc_start: 0.9125 (t80) cc_final: 0.8731 (t80) REVERT: A 668 MET cc_start: 0.9415 (mmp) cc_final: 0.9156 (mmm) REVERT: A 720 PHE cc_start: 0.9214 (t80) cc_final: 0.8903 (t80) REVERT: A 746 ARG cc_start: 0.9193 (ttm170) cc_final: 0.8861 (ptp-110) REVERT: A 811 LEU cc_start: 0.9087 (mt) cc_final: 0.8830 (mt) REVERT: A 868 ILE cc_start: 0.9089 (mt) cc_final: 0.8886 (mm) REVERT: A 870 ASP cc_start: 0.8934 (m-30) cc_final: 0.8686 (m-30) REVERT: A 949 MET cc_start: 0.6937 (pmm) cc_final: 0.6565 (pmm) REVERT: A 964 ARG cc_start: 0.6583 (mmt180) cc_final: 0.5098 (mmt180) REVERT: A 965 ASP cc_start: 0.8638 (t70) cc_final: 0.8180 (m-30) REVERT: A 975 ASN cc_start: 0.9360 (t0) cc_final: 0.9159 (m-40) REVERT: A 991 GLU cc_start: 0.9379 (mm-30) cc_final: 0.8984 (tm-30) REVERT: A 1100 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9351 (mm-30) REVERT: A 1250 MET cc_start: 0.8445 (mmm) cc_final: 0.7945 (mmm) outliers start: 33 outliers final: 28 residues processed: 203 average time/residue: 0.1061 time to fit residues: 30.3350 Evaluate side-chains 209 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 971 TRP Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.108268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.089390 restraints weight = 56030.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.091005 restraints weight = 43025.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.092207 restraints weight = 34755.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.093006 restraints weight = 29896.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.093516 restraints weight = 26922.354| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11016 Z= 0.150 Angle : 0.735 14.639 14960 Z= 0.379 Chirality : 0.042 0.234 1630 Planarity : 0.004 0.064 1786 Dihedral : 13.180 76.072 1797 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 3.09 % Allowed : 21.66 % Favored : 75.25 % 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: -0.48 (0.24), residues: 1187 helix: 0.47 (0.21), residues: 572 sheet: -0.90 (0.47), residues: 120 loop : -1.01 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.042 0.002 TYR A 807 PHE 0.033 0.002 PHE A 880 TRP 0.037 0.003 TRP A 609 HIS 0.005 0.001 HIS A1261 Details of bonding type rmsd covalent geometry : bond 0.00322 (11016) covalent geometry : angle 0.73514 (14960) hydrogen bonds : bond 0.04144 ( 476) hydrogen bonds : angle 4.72201 ( 1342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2199.35 seconds wall clock time: 38 minutes 45.86 seconds (2325.86 seconds total)