Starting phenix.real_space_refine on Fri Jul 3 00:34:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mku_48338/07_2026/9mku_48338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mku_48338/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mku_48338/07_2026/9mku_48338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mku_48338/07_2026/9mku_48338.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mku_48338/07_2026/9mku_48338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mku_48338/07_2026/9mku_48338.map" } 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-6108/lib/python3.11/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: 2.28, per 1000 atoms: 0.21 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: 0.91 Conformation dependent library (CDL) restraints added in 456.0 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: 1.50 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: 2.71 Time building geometry restraints manager: 1.19 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: 14884 2.76 - 5.51: 70 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=" N3 DT C -1 " pdb=" C4 DT C -1 " pdb=" O4 DT C -1 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C -8 " pdb=" C4 DT C -8 " pdb=" O4 DT C -8 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+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: 1420 0.059 - 0.118: 190 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: 2.140 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 12.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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= 0.184 Angle : 0.554 13.782 14960 Z= 0.370 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/Z covalent geometry : bond 0.00282 / 0.18 (11016) covalent geometry : angle 0.55444 / 0.37 (14960) hydrogen bonds : bond 0.16616 / 14.89 ( 476) hydrogen bonds : angle 6.03963 / 7.59 ( 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 : 0.329 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: 0.1147 time to fit residues: 50.5507 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 : 0.400 ------------------------------------------------------------------------------- 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... A 9 ASN A 188 ASN A 214 ASN A 274 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 424 GLN A 508 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 835 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.110841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.090229 restraints weight = 53045.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.092056 restraints weight = 41172.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.093283 restraints weight = 33519.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.094268 restraints weight = 28889.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.094968 restraints weight = 25758.580| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11016 Z= 0.166 Angle : 0.686 11.066 14960 Z= 0.365 Chirality : 0.043 0.242 1630 Planarity : 0.004 0.046 1786 Dihedral : 13.190 81.005 1798 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 3.00 % Allowed : 12.74 % Favored : 84.26 % 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: -0.29 (0.24), residues: 1187 helix: 0.49 (0.21), residues: 564 sheet: -0.38 (0.54), residues: 104 loop : -0.83 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 921 TYR 0.024 0.002 TYR A 807 PHE 0.024 0.002 PHE A 880 TRP 0.019 0.003 TRP A 734 HIS 0.005 0.002 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (11016) covalent geometry : angle 0.68563 / 0.37 (14960) hydrogen bonds : bond 0.05726 / 5.17 ( 476) hydrogen bonds : angle 5.16134 / 6.32 ( 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: 33 poor density : 231 time to evaluate : 0.330 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: symmetry clash REVERT: A 19 PHE cc_start: 0.9133 (m-80) cc_final: 0.8221 (m-80) REVERT: A 46 ASP cc_start: 0.9384 (m-30) cc_final: 0.9151 (t70) REVERT: A 61 PHE cc_start: 0.9191 (t80) cc_final: 0.8986 (t80) REVERT: A 65 ILE cc_start: 0.9409 (tp) cc_final: 0.9131 (pt) REVERT: A 138 LEU cc_start: 0.9251 (mt) cc_final: 0.9040 (mt) REVERT: A 269 PHE cc_start: 0.9438 (t80) cc_final: 0.9233 (t80) REVERT: A 312 ASN cc_start: 0.9080 (t0) cc_final: 0.8851 (m-40) REVERT: A 366 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9080 (pm20) REVERT: A 595 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8563 (mtpp) REVERT: A 647 LYS cc_start: 0.9487 (tppt) cc_final: 0.9241 (mmmt) REVERT: A 659 TYR cc_start: 0.9196 (t80) cc_final: 0.8767 (t80) REVERT: A 668 MET cc_start: 0.9543 (mmp) cc_final: 0.9189 (mmm) REVERT: A 746 ARG cc_start: 0.9256 (ttm170) cc_final: 0.8868 (ptp-110) REVERT: A 807 TYR cc_start: 0.9049 (m-80) cc_final: 0.8847 (m-80) REVERT: A 811 LEU cc_start: 0.9127 (mt) cc_final: 0.8868 (mt) REVERT: A 868 ILE cc_start: 0.9065 (mt) cc_final: 0.8840 (mm) REVERT: A 949 MET cc_start: 0.6154 (pmm) cc_final: 0.5925 (pmm) REVERT: A 971 TRP cc_start: 0.9414 (t60) cc_final: 0.9124 (t60) REVERT: A 976 ASN cc_start: 0.9000 (m-40) cc_final: 0.8033 (t0) REVERT: A 1007 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7003 (m-30) REVERT: A 1100 GLU cc_start: 0.9718 (mt-10) cc_final: 0.9365 (mm-30) REVERT: A 1250 MET cc_start: 0.8325 (mmm) cc_final: 0.7788 (mmm) outliers start: 33 outliers final: 21 residues processed: 247 average time/residue: 0.1003 time to fit residues: 33.9531 Evaluate side-chains 223 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 470 ASP 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 1190 CYS 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: 0.2980 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 117 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 305 ASN A 538 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.110739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.090498 restraints weight = 53378.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.092173 restraints weight = 41174.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.093570 restraints weight = 32971.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094505 restraints weight = 28070.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.095016 restraints weight = 25034.048| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11016 Z= 0.146 Angle : 0.667 12.145 14960 Z= 0.351 Chirality : 0.042 0.227 1630 Planarity : 0.004 0.088 1786 Dihedral : 13.127 80.340 1798 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 3.64 % Allowed : 14.83 % Favored : 81.53 % 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: -0.36 (0.24), residues: 1187 helix: 0.41 (0.21), residues: 567 sheet: -0.38 (0.54), residues: 104 loop : -0.85 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 43 TYR 0.027 0.002 TYR A1024 PHE 0.030 0.002 PHE A 880 TRP 0.030 0.003 TRP A 175 HIS 0.006 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (11016) covalent geometry : angle 0.66678 / 0.35 (14960) hydrogen bonds : bond 0.05009 / 4.62 ( 476) hydrogen bonds : angle 4.94859 / 6.05 ( 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 251 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.426 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: A 19 PHE cc_start: 0.9061 (m-80) cc_final: 0.8199 (m-80) REVERT: A 65 ILE cc_start: 0.9406 (tp) cc_final: 0.9089 (pt) REVERT: A 138 LEU cc_start: 0.9224 (mt) cc_final: 0.9018 (mt) REVERT: A 327 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: A 366 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9113 (pm20) REVERT: A 498 ASN cc_start: 0.9508 (t0) cc_final: 0.9171 (m-40) REVERT: A 595 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8656 (mtpp) REVERT: A 647 LYS cc_start: 0.9494 (tppt) cc_final: 0.9283 (mmmt) REVERT: A 659 TYR cc_start: 0.9196 (t80) cc_final: 0.8879 (t80) REVERT: A 746 ARG cc_start: 0.9219 (ttm170) cc_final: 0.8835 (ptp-110) REVERT: A 811 LEU cc_start: 0.9052 (mt) cc_final: 0.8802 (mt) REVERT: A 868 ILE cc_start: 0.9033 (mt) cc_final: 0.8780 (mm) REVERT: A 870 ASP cc_start: 0.8936 (m-30) cc_final: 0.8523 (t0) REVERT: A 949 MET cc_start: 0.6122 (pmm) cc_final: 0.5881 (pmm) REVERT: A 971 TRP cc_start: 0.9240 (t60) cc_final: 0.8929 (t60) REVERT: A 973 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8831 (mtpt) REVERT: A 976 ASN cc_start: 0.9097 (m-40) cc_final: 0.8143 (t0) REVERT: A 1007 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: A 1067 MET cc_start: 0.7101 (mtt) cc_final: 0.6859 (mmt) REVERT: A 1100 GLU cc_start: 0.9711 (mt-10) cc_final: 0.9362 (mm-30) REVERT: A 1250 MET cc_start: 0.8410 (mmm) cc_final: 0.7921 (mmm) REVERT: A 1289 GLU cc_start: 0.9181 (mp0) cc_final: 0.8833 (mp0) outliers start: 40 outliers final: 25 residues processed: 233 average time/residue: 0.0977 time to fit residues: 31.2606 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 202 ARG Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 295 THR 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 481 ASN Chi-restraints excluded: chain A residue 499 LEU 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 734 TRP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 973 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 chunk 30 optimal weight: 0.0570 chunk 97 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.110722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.090808 restraints weight = 55313.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.092600 restraints weight = 42665.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.093918 restraints weight = 34175.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.094599 restraints weight = 29195.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.095433 restraints weight = 26481.640| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3644 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= 0.145 Angle : 0.661 10.995 14960 Z= 0.346 Chirality : 0.042 0.340 1630 Planarity : 0.004 0.050 1786 Dihedral : 13.091 84.407 1797 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 3.46 % Allowed : 16.74 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1187 helix: 0.41 (0.21), residues: 567 sheet: -0.55 (0.52), residues: 106 loop : -0.92 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 202 TYR 0.040 0.002 TYR A 807 PHE 0.035 0.002 PHE A 211 TRP 0.044 0.003 TRP A 175 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (11016) covalent geometry : angle 0.66081 / 0.35 (14960) hydrogen bonds : bond 0.04749 / 4.34 ( 476) hydrogen bonds : angle 4.90950 / 6.07 ( 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 242 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.245 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: A 19 PHE cc_start: 0.9088 (m-80) cc_final: 0.8226 (m-80) REVERT: A 65 ILE cc_start: 0.9443 (tp) cc_final: 0.9165 (pt) REVERT: A 138 LEU cc_start: 0.9290 (mt) cc_final: 0.9081 (mt) REVERT: A 166 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9065 (mt) REVERT: A 352 MET cc_start: 0.9253 (mmp) cc_final: 0.9009 (mmp) REVERT: A 366 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9156 (pm20) REVERT: A 498 ASN cc_start: 0.9506 (t0) cc_final: 0.9191 (m-40) REVERT: A 538 HIS cc_start: 0.9542 (m-70) cc_final: 0.9211 (m-70) REVERT: A 595 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8812 (mtpp) REVERT: A 643 ASP cc_start: 0.9279 (p0) cc_final: 0.8851 (p0) REVERT: A 659 TYR cc_start: 0.9184 (t80) cc_final: 0.8709 (t80) REVERT: A 746 ARG cc_start: 0.9225 (ttm170) cc_final: 0.8856 (ptp-110) REVERT: A 811 LEU cc_start: 0.9045 (mt) cc_final: 0.8776 (mt) REVERT: A 870 ASP cc_start: 0.8796 (m-30) cc_final: 0.8360 (t0) REVERT: A 971 TRP cc_start: 0.9300 (t60) cc_final: 0.8937 (t60) REVERT: A 976 ASN cc_start: 0.9094 (m-40) cc_final: 0.8144 (t0) REVERT: A 1007 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: A 1100 GLU cc_start: 0.9702 (mt-10) cc_final: 0.9367 (mm-30) REVERT: A 1250 MET cc_start: 0.8405 (mmm) cc_final: 0.7863 (mmm) outliers start: 38 outliers final: 22 residues processed: 229 average time/residue: 0.1010 time to fit residues: 32.1890 Evaluate side-chains 214 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 202 ARG Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 327 GLN 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 499 LEU 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 973 LYS Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1027 LEU 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: 7.9990 chunk 46 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 0.0040 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4179 r_free = 0.4179 target = 0.114283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.093502 restraints weight = 52554.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.095802 restraints weight = 36245.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.097424 restraints weight = 27750.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.098551 restraints weight = 22695.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.099378 restraints weight = 19583.002| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4017 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= 0.136 Angle : 0.680 15.735 14960 Z= 0.349 Chirality : 0.042 0.292 1630 Planarity : 0.004 0.052 1786 Dihedral : 13.064 83.476 1797 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 3.18 % Allowed : 18.65 % Favored : 78.16 % 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: -0.41 (0.24), residues: 1187 helix: 0.47 (0.21), residues: 564 sheet: -0.48 (0.52), residues: 106 loop : -0.98 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.044 0.002 TYR A 807 PHE 0.032 0.002 PHE A 880 TRP 0.035 0.003 TRP A 175 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (11016) covalent geometry : angle 0.67988 / 0.35 (14960) hydrogen bonds : bond 0.04578 / 4.21 ( 476) hydrogen bonds : angle 4.74276 / 5.90 ( 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 238 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.438 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: 0.9167 (m-80) cc_final: 0.8303 (m-80) REVERT: A 65 ILE cc_start: 0.9429 (tp) cc_final: 0.9157 (pt) REVERT: A 138 LEU cc_start: 0.9335 (mt) cc_final: 0.9125 (mt) REVERT: A 166 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9077 (mt) REVERT: A 356 TYR cc_start: 0.9087 (t80) cc_final: 0.8864 (m-80) REVERT: A 366 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9158 (pm20) REVERT: A 475 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: A 498 ASN cc_start: 0.9494 (t0) cc_final: 0.9149 (m-40) REVERT: A 538 HIS cc_start: 0.9528 (m-70) cc_final: 0.9198 (m-70) REVERT: A 539 LYS cc_start: 0.9666 (mmtm) cc_final: 0.9435 (ptpp) REVERT: A 595 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8825 (mtpp) REVERT: A 627 LYS cc_start: 0.9341 (mtmm) cc_final: 0.9069 (pttm) REVERT: A 659 TYR cc_start: 0.9119 (t80) cc_final: 0.8709 (t80) REVERT: A 736 ASP cc_start: 0.9349 (m-30) cc_final: 0.9144 (p0) REVERT: A 746 ARG cc_start: 0.9206 (ttm170) cc_final: 0.8852 (ptp-110) REVERT: A 811 LEU cc_start: 0.9096 (mt) cc_final: 0.8832 (mt) REVERT: A 870 ASP cc_start: 0.8821 (m-30) cc_final: 0.8403 (t0) REVERT: A 971 TRP cc_start: 0.9276 (t60) cc_final: 0.8904 (t60) REVERT: A 976 ASN cc_start: 0.9097 (m-40) cc_final: 0.8127 (t0) REVERT: A 1007 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: A 1008 LEU cc_start: 0.5068 (mt) cc_final: 0.3915 (mm) REVERT: A 1100 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9349 (mm-30) REVERT: A 1250 MET cc_start: 0.8414 (mmm) cc_final: 0.7953 (mmm) outliers start: 35 outliers final: 26 residues processed: 223 average time/residue: 0.1049 time to fit residues: 32.5813 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 202 ARG Chi-restraints excluded: chain A residue 214 ASN 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 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 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 765 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 973 LYS Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1027 LEU 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: 6.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 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 = 0.4171 r_free = 0.4171 target = 0.114224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.093881 restraints weight = 53422.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.096006 restraints weight = 36548.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.097571 restraints weight = 28125.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.098635 restraints weight = 23085.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.099393 restraints weight = 19986.768| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11016 Z= 0.143 Angle : 0.674 13.708 14960 Z= 0.347 Chirality : 0.041 0.255 1630 Planarity : 0.003 0.051 1786 Dihedral : 13.039 82.492 1797 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 3.28 % Allowed : 19.20 % Favored : 77.53 % 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: -0.40 (0.24), residues: 1187 helix: 0.52 (0.21), residues: 562 sheet: -0.45 (0.52), residues: 106 loop : -1.04 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.039 0.002 TYR A 807 PHE 0.032 0.002 PHE A 880 TRP 0.017 0.002 TRP A 175 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (11016) covalent geometry : angle 0.67356 / 0.35 (14960) hydrogen bonds : bond 0.04437 / 4.02 ( 476) hydrogen bonds : angle 4.71684 / 5.81 ( 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 235 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.429 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: 0.9204 (m-80) cc_final: 0.8346 (m-80) REVERT: A 65 ILE cc_start: 0.9434 (tp) cc_final: 0.9111 (pt) REVERT: A 138 LEU cc_start: 0.9350 (mt) cc_final: 0.9144 (mt) REVERT: A 166 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9074 (mt) REVERT: A 366 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9159 (pm20) REVERT: A 392 TYR cc_start: 0.9574 (OUTLIER) cc_final: 0.9222 (t80) REVERT: A 475 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7481 (m-10) REVERT: A 498 ASN cc_start: 0.9496 (t0) cc_final: 0.9152 (m-40) REVERT: A 538 HIS cc_start: 0.9532 (m-70) cc_final: 0.9184 (m-70) REVERT: A 539 LYS cc_start: 0.9666 (mmtm) cc_final: 0.9464 (ptpp) REVERT: A 595 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8846 (mtpp) REVERT: A 659 TYR cc_start: 0.9218 (t80) cc_final: 0.8685 (t80) REVERT: A 736 ASP cc_start: 0.9363 (m-30) cc_final: 0.9135 (p0) REVERT: A 746 ARG cc_start: 0.9215 (ttm170) cc_final: 0.8860 (ptp-110) REVERT: A 811 LEU cc_start: 0.9100 (mt) cc_final: 0.8829 (mt) REVERT: A 870 ASP cc_start: 0.8771 (m-30) cc_final: 0.8346 (t0) REVERT: A 971 TRP cc_start: 0.9278 (t60) cc_final: 0.8926 (t60) REVERT: A 976 ASN cc_start: 0.9143 (m-40) cc_final: 0.8159 (t0) REVERT: A 1007 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: A 1008 LEU cc_start: 0.4965 (mt) cc_final: 0.4036 (mt) REVERT: A 1100 GLU cc_start: 0.9686 (mt-10) cc_final: 0.9350 (mm-30) REVERT: A 1250 MET cc_start: 0.8424 (mmm) cc_final: 0.7917 (mmm) outliers start: 36 outliers final: 28 residues processed: 218 average time/residue: 0.1034 time to fit residues: 31.5144 Evaluate side-chains 220 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 191 SER 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 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 PHE 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 885 THR Chi-restraints excluded: chain A residue 913 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** A 894 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 = 0.4131 r_free = 0.4131 target = 0.110661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.091015 restraints weight = 53806.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.093075 restraints weight = 36458.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.094593 restraints weight = 27927.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.095603 restraints weight = 23009.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.096316 restraints weight = 19928.612| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11016 Z= 0.190 Angle : 0.698 13.902 14960 Z= 0.369 Chirality : 0.042 0.251 1630 Planarity : 0.004 0.097 1786 Dihedral : 13.178 80.591 1797 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 4.46 % Allowed : 19.11 % 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: -0.54 (0.24), residues: 1187 helix: 0.44 (0.21), residues: 565 sheet: -0.96 (0.49), residues: 121 loop : -1.04 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 202 TYR 0.036 0.002 TYR A 807 PHE 0.034 0.002 PHE A 880 TRP 0.034 0.003 TRP A 175 HIS 0.004 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (11016) covalent geometry : angle 0.69783 / 0.37 (14960) hydrogen bonds : bond 0.04589 / 4.19 ( 476) hydrogen bonds : angle 4.93603 / 6.09 ( 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 245 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.371 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: A 19 PHE cc_start: 0.9185 (m-80) cc_final: 0.8345 (m-80) REVERT: A 32 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8348 (mmtt) REVERT: A 65 ILE cc_start: 0.9378 (tp) cc_final: 0.9130 (pt) REVERT: A 166 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9048 (mt) REVERT: A 175 TRP cc_start: 0.8237 (m-10) cc_final: 0.7681 (m-10) REVERT: A 366 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9259 (pm20) REVERT: A 392 TYR cc_start: 0.9629 (OUTLIER) cc_final: 0.9354 (t80) REVERT: A 475 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: A 494 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: A 602 ASN cc_start: 0.8029 (t0) cc_final: 0.7752 (t0) REVERT: A 659 TYR cc_start: 0.9218 (t80) cc_final: 0.8767 (t80) REVERT: A 746 ARG cc_start: 0.9241 (ttm170) cc_final: 0.8910 (ptp-110) REVERT: A 811 LEU cc_start: 0.9164 (mt) cc_final: 0.8881 (mt) REVERT: A 870 ASP cc_start: 0.8777 (m-30) cc_final: 0.8327 (t0) REVERT: A 949 MET cc_start: 0.6708 (pmm) cc_final: 0.6328 (pmm) REVERT: A 965 ASP cc_start: 0.8342 (t70) cc_final: 0.7774 (m-30) REVERT: A 971 TRP cc_start: 0.9313 (t60) cc_final: 0.8960 (t60) REVERT: A 976 ASN cc_start: 0.9203 (m-40) cc_final: 0.8170 (t0) REVERT: A 1100 GLU cc_start: 0.9674 (mt-10) cc_final: 0.9338 (mm-30) REVERT: A 1250 MET cc_start: 0.8492 (mmm) cc_final: 0.7935 (mmm) REVERT: A 1264 LEU cc_start: 0.8738 (tp) cc_final: 0.8511 (mt) outliers start: 49 outliers final: 37 residues processed: 221 average time/residue: 0.0963 time to fit residues: 30.1858 Evaluate side-chains 229 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 197 THR 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 300 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR 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 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 PHE 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 973 LYS 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 1039 VAL Chi-restraints excluded: chain A residue 1070 GLN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS ** A 207 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 = 0.4148 r_free = 0.4148 target = 0.110777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.090136 restraints weight = 52598.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.092427 restraints weight = 36293.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.094001 restraints weight = 27647.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.095094 restraints weight = 22593.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.095903 restraints weight = 19497.987| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4544 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= 0.149 Angle : 0.692 14.415 14960 Z= 0.360 Chirality : 0.043 0.322 1630 Planarity : 0.004 0.053 1786 Dihedral : 13.182 80.381 1797 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 3.73 % Allowed : 20.29 % Favored : 75.98 % 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: -0.54 (0.24), residues: 1187 helix: 0.44 (0.21), residues: 566 sheet: -0.92 (0.49), residues: 120 loop : -1.04 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1272 TYR 0.042 0.002 TYR A 807 PHE 0.033 0.002 PHE A1294 TRP 0.029 0.003 TRP A 609 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (11016) covalent geometry : angle 0.69211 / 0.36 (14960) hydrogen bonds : bond 0.04513 / 4.14 ( 476) hydrogen bonds : angle 4.82349 / 5.96 ( 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 233 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.458 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: A 19 PHE cc_start: 0.9170 (m-80) cc_final: 0.8328 (m-80) REVERT: A 32 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8246 (mmtt) REVERT: A 65 ILE cc_start: 0.9371 (tp) cc_final: 0.9123 (pt) REVERT: A 118 LYS cc_start: 0.8883 (tptt) cc_final: 0.8647 (tptt) REVERT: A 166 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9042 (mt) REVERT: A 275 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8091 (mm-40) REVERT: A 366 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9240 (pm20) REVERT: A 392 TYR cc_start: 0.9628 (OUTLIER) cc_final: 0.9397 (t80) REVERT: A 475 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7593 (m-10) REVERT: A 494 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: A 538 HIS cc_start: 0.9564 (m-70) cc_final: 0.9201 (m-70) REVERT: A 602 ASN cc_start: 0.7998 (t0) cc_final: 0.7654 (t0) REVERT: A 659 TYR cc_start: 0.9192 (t80) cc_final: 0.8761 (t80) REVERT: A 746 ARG cc_start: 0.9221 (ttm170) cc_final: 0.8900 (ptp-110) REVERT: A 811 LEU cc_start: 0.9146 (mt) cc_final: 0.8877 (mt) REVERT: A 870 ASP cc_start: 0.8742 (m-30) cc_final: 0.8297 (t0) REVERT: A 949 MET cc_start: 0.6554 (pmm) cc_final: 0.6197 (pmm) REVERT: A 971 TRP cc_start: 0.9279 (t60) cc_final: 0.8970 (t60) REVERT: A 976 ASN cc_start: 0.9184 (m-40) cc_final: 0.8210 (t0) REVERT: A 1100 GLU cc_start: 0.9671 (mt-10) cc_final: 0.9329 (mm-30) REVERT: A 1250 MET cc_start: 0.8483 (mmm) cc_final: 0.7939 (mmm) outliers start: 41 outliers final: 32 residues processed: 212 average time/residue: 0.1009 time to fit residues: 30.2102 Evaluate side-chains 220 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 199 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR 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 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 PHE 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 928 LEU 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 1172 LYS 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: 6.9990 chunk 40 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 117 optimal weight: 0.0980 chunk 114 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** 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 = 0.4171 r_free = 0.4171 target = 0.112981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.092241 restraints weight = 51563.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.094523 restraints weight = 36208.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.096079 restraints weight = 27710.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.097186 restraints weight = 22781.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.098012 restraints weight = 19675.970| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4666 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= 0.133 Angle : 0.709 15.182 14960 Z= 0.364 Chirality : 0.043 0.374 1630 Planarity : 0.004 0.062 1786 Dihedral : 13.113 80.483 1797 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 3.18 % Allowed : 21.02 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1187 helix: 0.48 (0.21), residues: 564 sheet: -0.61 (0.50), residues: 113 loop : -1.07 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1218 TYR 0.043 0.002 TYR A 807 PHE 0.033 0.002 PHE A1294 TRP 0.037 0.003 TRP A 609 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (11016) covalent geometry : angle 0.70901 / 0.36 (14960) hydrogen bonds : bond 0.04288 / 3.92 ( 476) hydrogen bonds : angle 4.64664 / 5.76 ( 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 229 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.305 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: A 10 LYS cc_start: 0.9404 (mmmt) cc_final: 0.9154 (mmmt) REVERT: A 19 PHE cc_start: 0.9206 (m-80) cc_final: 0.8338 (m-80) REVERT: A 32 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8307 (mmtt) REVERT: A 65 ILE cc_start: 0.9393 (tp) cc_final: 0.9131 (pt) REVERT: A 138 LEU cc_start: 0.9390 (mt) cc_final: 0.9188 (mt) REVERT: A 166 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9057 (mt) REVERT: A 366 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9233 (pm20) REVERT: A 392 TYR cc_start: 0.9648 (OUTLIER) cc_final: 0.9404 (t80) REVERT: A 475 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7611 (m-10) REVERT: A 487 MET cc_start: 0.9206 (ptp) cc_final: 0.8956 (pmm) REVERT: A 494 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: A 498 ASN cc_start: 0.9540 (t0) cc_final: 0.9180 (m-40) REVERT: A 538 HIS cc_start: 0.9601 (m-70) cc_final: 0.9252 (m-70) REVERT: A 602 ASN cc_start: 0.7858 (t0) cc_final: 0.7579 (t0) REVERT: A 659 TYR cc_start: 0.9188 (t80) cc_final: 0.8682 (t80) REVERT: A 746 ARG cc_start: 0.9204 (ttm170) cc_final: 0.8886 (ptp-110) REVERT: A 811 LEU cc_start: 0.9131 (mt) cc_final: 0.8871 (mt) REVERT: A 870 ASP cc_start: 0.8792 (m-30) cc_final: 0.8356 (t0) REVERT: A 965 ASP cc_start: 0.8346 (t70) cc_final: 0.7747 (m-30) REVERT: A 971 TRP cc_start: 0.9183 (t60) cc_final: 0.8841 (t60) REVERT: A 976 ASN cc_start: 0.9122 (m-40) cc_final: 0.8193 (t0) REVERT: A 1007 ASP cc_start: 0.8941 (t0) cc_final: 0.8332 (m-30) REVERT: A 1100 GLU cc_start: 0.9698 (mt-10) cc_final: 0.9356 (mm-30) REVERT: A 1250 MET cc_start: 0.8421 (mmm) cc_final: 0.7877 (mmm) outliers start: 35 outliers final: 28 residues processed: 211 average time/residue: 0.1041 time to fit residues: 31.1041 Evaluate side-chains 218 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 PHE 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 885 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** 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 = 0.4149 r_free = 0.4149 target = 0.112624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.092803 restraints weight = 51980.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.094936 restraints weight = 36675.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.096429 restraints weight = 28311.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.097466 restraints weight = 23397.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.098179 restraints weight = 20287.605| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4780 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= 0.137 Angle : 0.708 15.042 14960 Z= 0.365 Chirality : 0.043 0.332 1630 Planarity : 0.004 0.049 1786 Dihedral : 13.120 79.759 1797 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 3.00 % Allowed : 21.38 % Favored : 75.61 % 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: -0.53 (0.24), residues: 1187 helix: 0.47 (0.21), residues: 567 sheet: -0.66 (0.50), residues: 113 loop : -1.15 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1272 TYR 0.042 0.002 TYR A 807 PHE 0.037 0.002 PHE A 880 TRP 0.043 0.003 TRP A 609 HIS 0.003 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (11016) covalent geometry : angle 0.70843 / 0.37 (14960) hydrogen bonds : bond 0.04305 / 3.93 ( 476) hydrogen bonds : angle 4.67927 / 5.77 ( 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 : 0.312 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: A 10 LYS cc_start: 0.9419 (mmmt) cc_final: 0.9161 (mmmt) REVERT: A 19 PHE cc_start: 0.9222 (m-80) cc_final: 0.8348 (m-80) REVERT: A 32 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8300 (mmtt) REVERT: A 65 ILE cc_start: 0.9400 (tp) cc_final: 0.9144 (pt) REVERT: A 118 LYS cc_start: 0.8856 (tptt) cc_final: 0.8630 (tptt) REVERT: A 138 LEU cc_start: 0.9389 (mt) cc_final: 0.9179 (mt) REVERT: A 166 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9064 (mt) REVERT: A 366 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9241 (pm20) REVERT: A 392 TYR cc_start: 0.9654 (OUTLIER) cc_final: 0.9441 (t80) REVERT: A 463 PHE cc_start: 0.9714 (t80) cc_final: 0.9442 (m-80) REVERT: A 475 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: A 487 MET cc_start: 0.9214 (ptp) cc_final: 0.8966 (pmm) REVERT: A 494 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: A 498 ASN cc_start: 0.9545 (t0) cc_final: 0.9182 (m-40) REVERT: A 602 ASN cc_start: 0.7937 (t0) cc_final: 0.7542 (t0) REVERT: A 659 TYR cc_start: 0.9213 (t80) cc_final: 0.8716 (t80) REVERT: A 746 ARG cc_start: 0.9203 (ttm170) cc_final: 0.8874 (ptp-110) REVERT: A 811 LEU cc_start: 0.9168 (mt) cc_final: 0.8892 (mt) REVERT: A 870 ASP cc_start: 0.8800 (m-30) cc_final: 0.8358 (t0) REVERT: A 964 ARG cc_start: 0.7675 (mmt180) cc_final: 0.6482 (mmt180) REVERT: A 971 TRP cc_start: 0.9244 (t60) cc_final: 0.8878 (t60) REVERT: A 976 ASN cc_start: 0.9115 (m-40) cc_final: 0.8156 (t0) REVERT: A 1007 ASP cc_start: 0.8864 (t0) cc_final: 0.8293 (m-30) REVERT: A 1100 GLU cc_start: 0.9712 (mt-10) cc_final: 0.9360 (mm-30) REVERT: A 1250 MET cc_start: 0.8439 (mmm) cc_final: 0.7885 (mmm) outliers start: 33 outliers final: 29 residues processed: 200 average time/residue: 0.1031 time to fit residues: 29.2533 Evaluate side-chains 213 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 288 LYS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 499 LEU 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 641 PHE 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 1031 LEU Chi-restraints excluded: chain A residue 1062 GLU 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: 2.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 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 = 0.4117 r_free = 0.4117 target = 0.108832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.089507 restraints weight = 53221.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.091456 restraints weight = 37617.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.092850 restraints weight = 29420.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.093864 restraints weight = 24424.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.094576 restraints weight = 21248.398| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11016 Z= 0.175 Angle : 0.718 13.923 14960 Z= 0.377 Chirality : 0.043 0.287 1630 Planarity : 0.004 0.051 1786 Dihedral : 13.241 78.304 1797 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.93 % 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: -0.71 (0.23), residues: 1187 helix: 0.35 (0.21), residues: 568 sheet: -1.15 (0.47), residues: 122 loop : -1.17 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1272 TYR 0.040 0.002 TYR A 807 PHE 0.034 0.002 PHE A 880 TRP 0.043 0.004 TRP A 609 HIS 0.004 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (11016) covalent geometry : angle 0.71757 / 0.38 (14960) hydrogen bonds : bond 0.04539 / 4.09 ( 476) hydrogen bonds : angle 4.86888 / 6.00 ( 1342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.82 seconds wall clock time: 35 minutes 46.51 seconds (2146.51 seconds total)