Starting phenix.real_space_refine on Wed Aug 5 23:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6t_41080/08_2026/8t6t_41080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6t_41080/08_2026/8t6t_41080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t6t_41080/08_2026/8t6t_41080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6t_41080/08_2026/8t6t_41080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6t_41080/08_2026/8t6t_41080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6t_41080/08_2026/8t6t_41080.map" } resolution = 3.04 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= 0.011 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 126 5.49 5 S 18 5.16 5 C 7378 2.51 5 N 2160 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12306 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9585 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 33, 'TRANS': 1134} Chain breaks: 5 Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2035 Classifications: {'RNA': 95} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 84} Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 2.82, per 1000 atoms: 0.23 Number of scatterers: 12306 At special positions: 0 Unit cell: (87.486, 129.979, 122.48, 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 18 16.00 P 126 15.00 O 2624 8.00 N 2160 7.00 C 7378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 601.4 milliseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 52.9% alpha, 8.3% beta 45 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.859A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.910A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.810A pdb=" N ASP A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.603A pdb=" N LEU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 5.207A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.659A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 4.139A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.652A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.042A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.057A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.855A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.686A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.950A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.801A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.513A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.302A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.839A pdb=" N HIS A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.182A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.450A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A1000 " --> pdb=" O ALA A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.843A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 4.747A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.501A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.568A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.680A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 958 removed outlier: 6.199A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.466A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU A1214 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN A1221 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.893A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.515A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.186A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1325 419 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2643 1.33 - 1.45: 3315 1.45 - 1.57: 6559 1.57 - 1.69: 255 1.69 - 1.81: 35 Bond restraints: 12807 Sorted by residual: bond pdb=" N9 DA D 43 " pdb=" C4 DA D 43 " ideal model delta sigma weight residual 1.374 1.347 0.027 6.00e-03 2.78e+04 2.06e+01 bond pdb=" N9 DG C 20 " pdb=" C4 DG C 20 " ideal model delta sigma weight residual 1.375 1.340 0.035 8.00e-03 1.56e+04 1.90e+01 bond pdb=" C5' DA D 43 " pdb=" C4' DA D 43 " ideal model delta sigma weight residual 1.512 1.483 0.029 7.00e-03 2.04e+04 1.71e+01 bond pdb=" C2 DG C 20 " pdb=" N3 DG C 20 " ideal model delta sigma weight residual 1.323 1.291 0.032 8.00e-03 1.56e+04 1.58e+01 bond pdb=" C1' DT D 42 " pdb=" N1 DT D 42 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.55e+01 ... (remaining 12802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 17642 5.16 - 10.32: 150 10.32 - 15.48: 44 15.48 - 20.65: 7 20.65 - 25.81: 1 Bond angle restraints: 17844 Sorted by residual: angle pdb=" O4' DA D 40 " pdb=" C1' DA D 40 " pdb=" N9 DA D 40 " ideal model delta sigma weight residual 108.00 123.40 -15.40 7.00e-01 2.04e+00 4.84e+02 angle pdb=" O4' DC C 21 " pdb=" C1' DC C 21 " pdb=" N1 DC C 21 " ideal model delta sigma weight residual 108.00 121.06 -13.06 7.00e-01 2.04e+00 3.48e+02 angle pdb=" O4' DG D 41 " pdb=" C1' DG D 41 " pdb=" N9 DG D 41 " ideal model delta sigma weight residual 108.00 120.32 -12.32 7.00e-01 2.04e+00 3.10e+02 angle pdb=" O4' DA C 14 " pdb=" C1' DA C 14 " pdb=" N9 DA C 14 " ideal model delta sigma weight residual 108.00 118.96 -10.96 7.00e-01 2.04e+00 2.45e+02 angle pdb=" O4' DC D 39 " pdb=" C1' DC D 39 " pdb=" N1 DC D 39 " ideal model delta sigma weight residual 108.00 118.91 -10.91 7.00e-01 2.04e+00 2.43e+02 ... (remaining 17839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 7336 33.38 - 66.76: 423 66.76 - 100.14: 36 100.14 - 133.52: 2 133.52 - 166.90: 4 Dihedral angle restraints: 7801 sinusoidal: 4363 harmonic: 3438 Sorted by residual: dihedral pdb=" CA ASN A 726 " pdb=" C ASN A 726 " pdb=" N LEU A 727 " pdb=" CA LEU A 727 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLU A1056 " pdb=" C GLU A1056 " pdb=" N ILE A1057 " pdb=" CA ILE A1057 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE A1057 " pdb=" C ILE A1057 " pdb=" N ARG A1058 " pdb=" CA ARG A1058 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 2012 0.253 - 0.505: 25 0.505 - 0.758: 7 0.758 - 1.011: 5 1.011 - 1.263: 6 Chirality restraints: 2055 Sorted by residual: chirality pdb=" C1' DC D 39 " pdb=" O4' DC D 39 " pdb=" C2' DC D 39 " pdb=" N1 DC D 39 " both_signs ideal model delta sigma weight residual False 2.43 1.17 1.26 2.00e-01 2.50e+01 3.99e+01 chirality pdb=" C1' DC C 21 " pdb=" O4' DC C 21 " pdb=" C2' DC C 21 " pdb=" N1 DC C 21 " both_signs ideal model delta sigma weight residual False 2.43 1.21 1.22 2.00e-01 2.50e+01 3.71e+01 chirality pdb=" C1' DG D 41 " pdb=" O4' DG D 41 " pdb=" C2' DG D 41 " pdb=" N9 DG D 41 " both_signs ideal model delta sigma weight residual False 2.43 1.34 1.09 2.00e-01 2.50e+01 2.96e+01 ... (remaining 2052 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 12 " -0.056 2.00e-02 2.50e+03 2.48e-02 1.85e+01 pdb=" N9 DG C 12 " 0.051 2.00e-02 2.50e+03 pdb=" C8 DG C 12 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DG C 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 12 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG C 12 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG C 12 " -0.034 2.00e-02 2.50e+03 pdb=" N1 DG C 12 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 12 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG C 12 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG C 12 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG C 12 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 15 " -0.055 2.00e-02 2.50e+03 2.62e-02 1.55e+01 pdb=" N1 DC C 15 " 0.038 2.00e-02 2.50e+03 pdb=" C2 DC C 15 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC C 15 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC C 15 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC C 15 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC C 15 " -0.021 2.00e-02 2.50e+03 pdb=" C5 DC C 15 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC C 15 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " -0.048 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" N9 DG C 17 " 0.047 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " -0.020 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " 0.009 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.006 2.00e-02 2.50e+03 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1687 2.76 - 3.29: 11492 3.29 - 3.83: 21918 3.83 - 4.36: 26310 4.36 - 4.90: 40799 Nonbonded interactions: 102206 Sorted by model distance: nonbonded pdb=" O GLN A 83 " pdb=" OG SER A 87 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 474 " pdb=" OD1 ASN A 477 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.286 3.040 ... (remaining 102201 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12807 Z= 0.379 Angle : 1.378 25.807 17844 Z= 0.966 Chirality : 0.109 1.263 2055 Planarity : 0.005 0.055 1798 Dihedral : 18.875 166.901 5571 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 9.43 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1156 helix: -0.72 (0.21), residues: 516 sheet: -1.81 (0.45), residues: 110 loop : -1.10 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 635 TYR 0.025 0.002 TYR A 973 PHE 0.025 0.003 PHE A 553 TRP 0.031 0.003 TRP A1136 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.38 (12807) covalent geometry : angle 1.37774 / 0.97 (17844) hydrogen bonds : bond 0.13962 / 9.08 ( 529) hydrogen bonds : angle 6.03477 / 4.37 ( 1434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8189 (tpp80) REVERT: A 631 MET cc_start: 0.7538 (mtm) cc_final: 0.7157 (mtm) REVERT: A 1148 LYS cc_start: 0.8914 (mptt) cc_final: 0.8582 (mmtp) REVERT: A 1269 ILE cc_start: 0.9593 (mt) cc_final: 0.9384 (mt) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.1333 time to fit residues: 14.1481 Evaluate side-chains 56 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1241 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 10.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN A 341 GLN A 420 HIS A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067301 restraints weight = 25167.195| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.86 r_work: 0.2796 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12807 Z= 0.192 Angle : 0.666 8.780 17844 Z= 0.365 Chirality : 0.045 0.367 2055 Planarity : 0.004 0.056 1798 Dihedral : 20.041 175.076 3076 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.81 % Allowed : 9.05 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1156 helix: -0.12 (0.22), residues: 520 sheet: -1.68 (0.45), residues: 110 loop : -1.02 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 654 TYR 0.015 0.001 TYR A 362 PHE 0.010 0.001 PHE A1046 TRP 0.016 0.001 TRP A1136 HIS 0.003 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (12807) covalent geometry : angle 0.66627 / 0.37 (17844) hydrogen bonds : bond 0.05710 / 3.85 ( 529) hydrogen bonds : angle 5.05525 / 3.62 ( 1434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7006 (ptp) REVERT: A 652 LYS cc_start: 0.8857 (ptmt) cc_final: 0.8451 (pptt) REVERT: A 654 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.8067 (tpp-160) REVERT: A 1148 LYS cc_start: 0.9036 (mptt) cc_final: 0.8782 (mmtm) outliers start: 19 outliers final: 12 residues processed: 76 average time/residue: 0.1055 time to fit residues: 11.8146 Evaluate side-chains 70 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.118660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.067070 restraints weight = 25400.599| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.85 r_work: 0.2787 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12807 Z= 0.191 Angle : 0.608 8.194 17844 Z= 0.331 Chirality : 0.044 0.483 2055 Planarity : 0.004 0.054 1798 Dihedral : 20.084 179.231 3074 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.00 % Allowed : 10.86 % Favored : 87.14 % 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: -0.75 (0.24), residues: 1156 helix: 0.19 (0.22), residues: 528 sheet: -1.43 (0.47), residues: 104 loop : -0.91 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.020 0.001 TYR A1242 PHE 0.008 0.001 PHE A 290 TRP 0.012 0.001 TRP A 476 HIS 0.004 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (12807) covalent geometry : angle 0.60845 / 0.33 (17844) hydrogen bonds : bond 0.05025 / 3.42 ( 529) hydrogen bonds : angle 4.71474 / 3.39 ( 1434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7036 (ptp) REVERT: A 652 LYS cc_start: 0.8693 (ptmt) cc_final: 0.8479 (pptt) REVERT: A 654 ARG cc_start: 0.8374 (tpp-160) cc_final: 0.8169 (tpp-160) REVERT: A 1148 LYS cc_start: 0.8996 (mptt) cc_final: 0.8201 (mmmt) outliers start: 21 outliers final: 14 residues processed: 75 average time/residue: 0.1126 time to fit residues: 12.1827 Evaluate side-chains 70 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.120088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068531 restraints weight = 25167.834| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.85 r_work: 0.2819 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12807 Z= 0.132 Angle : 0.550 8.209 17844 Z= 0.300 Chirality : 0.042 0.371 2055 Planarity : 0.003 0.053 1798 Dihedral : 20.114 177.415 3074 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.19 % Allowed : 11.05 % Favored : 86.76 % 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: -0.49 (0.24), residues: 1156 helix: 0.47 (0.22), residues: 535 sheet: -1.37 (0.48), residues: 104 loop : -0.85 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1317 TYR 0.012 0.001 TYR A 155 PHE 0.014 0.001 PHE A 518 TRP 0.010 0.001 TRP A 476 HIS 0.003 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12807) covalent geometry : angle 0.54992 / 0.30 (17844) hydrogen bonds : bond 0.04433 / 3.03 ( 529) hydrogen bonds : angle 4.53279 / 3.24 ( 1434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8190 (pp30) REVERT: A 390 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8740 (mm) REVERT: A 511 HIS cc_start: 0.8334 (m90) cc_final: 0.7998 (m-70) REVERT: A 649 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8940 (mmmm) REVERT: A 652 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8061 (pttp) REVERT: A 654 ARG cc_start: 0.8428 (tpp-160) cc_final: 0.7993 (tpp-160) REVERT: A 1148 LYS cc_start: 0.9028 (mptt) cc_final: 0.8755 (mmtp) outliers start: 23 outliers final: 13 residues processed: 83 average time/residue: 0.1147 time to fit residues: 13.6124 Evaluate side-chains 73 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.116934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064769 restraints weight = 25633.636| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.90 r_work: 0.2734 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 12807 Z= 0.347 Angle : 0.683 8.954 17844 Z= 0.359 Chirality : 0.048 0.459 2055 Planarity : 0.004 0.048 1798 Dihedral : 20.003 178.783 3074 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.10 % Allowed : 12.29 % Favored : 85.62 % 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: -0.65 (0.23), residues: 1156 helix: 0.35 (0.22), residues: 544 sheet: -1.48 (0.47), residues: 104 loop : -0.96 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 340 TYR 0.024 0.002 TYR A 362 PHE 0.015 0.002 PHE A 518 TRP 0.012 0.002 TRP A 476 HIS 0.007 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.35 (12807) covalent geometry : angle 0.68315 / 0.36 (17844) hydrogen bonds : bond 0.05236 / 3.59 ( 529) hydrogen bonds : angle 4.64954 / 3.34 ( 1434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 HIS cc_start: 0.8315 (m90) cc_final: 0.7965 (m-70) REVERT: A 649 LYS cc_start: 0.9201 (mmtm) cc_final: 0.8930 (mmmm) REVERT: A 652 LYS cc_start: 0.8720 (ptmt) cc_final: 0.8172 (pttp) REVERT: A 654 ARG cc_start: 0.8429 (tpp-160) cc_final: 0.7951 (tpp-160) REVERT: A 1148 LYS cc_start: 0.9032 (mptt) cc_final: 0.8740 (mmtp) REVERT: A 1303 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8383 (ttm170) outliers start: 22 outliers final: 17 residues processed: 75 average time/residue: 0.1084 time to fit residues: 11.7127 Evaluate side-chains 75 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.119148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067177 restraints weight = 25290.352| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.89 r_work: 0.2791 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12807 Z= 0.143 Angle : 0.555 7.938 17844 Z= 0.301 Chirality : 0.041 0.398 2055 Planarity : 0.003 0.048 1798 Dihedral : 20.054 176.021 3074 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.00 % Allowed : 12.76 % Favored : 85.24 % 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: 1156 helix: 0.54 (0.22), residues: 544 sheet: -1.44 (0.47), residues: 104 loop : -0.80 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1122 TYR 0.014 0.001 TYR A 155 PHE 0.040 0.001 PHE A 518 TRP 0.012 0.001 TRP A 476 HIS 0.003 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12807) covalent geometry : angle 0.55524 / 0.30 (17844) hydrogen bonds : bond 0.04490 / 3.06 ( 529) hydrogen bonds : angle 4.50067 / 3.21 ( 1434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.5973 (pt0) REVERT: A 390 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8749 (mm) REVERT: A 649 LYS cc_start: 0.9210 (mmtm) cc_final: 0.8902 (mmmm) REVERT: A 652 LYS cc_start: 0.8693 (ptmt) cc_final: 0.8154 (pttp) REVERT: A 654 ARG cc_start: 0.8400 (tpp-160) cc_final: 0.7926 (tpp-160) REVERT: A 662 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7968 (pp) REVERT: A 1148 LYS cc_start: 0.8996 (mptt) cc_final: 0.8685 (mmtp) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 0.1201 time to fit residues: 13.3413 Evaluate side-chains 77 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 983 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.119962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068314 restraints weight = 25111.319| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.87 r_work: 0.2817 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12807 Z= 0.126 Angle : 0.538 9.498 17844 Z= 0.290 Chirality : 0.041 0.390 2055 Planarity : 0.003 0.050 1798 Dihedral : 19.962 175.373 3074 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.10 % Allowed : 13.24 % Favored : 84.67 % 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: -0.20 (0.24), residues: 1156 helix: 0.69 (0.22), residues: 544 sheet: -1.32 (0.48), residues: 104 loop : -0.67 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1122 TYR 0.014 0.001 TYR A1242 PHE 0.035 0.001 PHE A 518 TRP 0.010 0.001 TRP A 476 HIS 0.002 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (12807) covalent geometry : angle 0.53756 / 0.29 (17844) hydrogen bonds : bond 0.04213 / 2.88 ( 529) hydrogen bonds : angle 4.39043 / 3.13 ( 1434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.5968 (pt0) REVERT: A 390 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8778 (mm) REVERT: A 511 HIS cc_start: 0.8319 (m90) cc_final: 0.7933 (m-70) REVERT: A 649 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8910 (mmmm) REVERT: A 652 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8187 (pttp) REVERT: A 654 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.7950 (tpp-160) REVERT: A 662 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 1148 LYS cc_start: 0.9054 (mptt) cc_final: 0.8733 (mmtp) outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 0.1240 time to fit residues: 14.1950 Evaluate side-chains 78 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.120214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.068449 restraints weight = 25031.461| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.87 r_work: 0.2823 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12807 Z= 0.126 Angle : 0.541 8.492 17844 Z= 0.289 Chirality : 0.041 0.394 2055 Planarity : 0.003 0.048 1798 Dihedral : 19.874 175.160 3074 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.81 % Allowed : 13.52 % Favored : 84.67 % 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: -0.14 (0.24), residues: 1156 helix: 0.74 (0.22), residues: 547 sheet: -1.17 (0.49), residues: 104 loop : -0.70 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.014 0.001 TYR A 155 PHE 0.006 0.001 PHE A 518 TRP 0.009 0.001 TRP A 476 HIS 0.002 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (12807) covalent geometry : angle 0.54080 / 0.29 (17844) hydrogen bonds : bond 0.04137 / 2.83 ( 529) hydrogen bonds : angle 4.34644 / 3.09 ( 1434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.5967 (pt0) REVERT: A 390 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8803 (mm) REVERT: A 511 HIS cc_start: 0.8369 (m90) cc_final: 0.7968 (m-70) REVERT: A 649 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8917 (mmmm) REVERT: A 652 LYS cc_start: 0.8736 (ptmt) cc_final: 0.8233 (pttp) REVERT: A 654 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.7956 (tpp-160) REVERT: A 662 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7741 (pp) REVERT: A 1148 LYS cc_start: 0.9068 (mptt) cc_final: 0.8731 (mmtp) REVERT: A 1252 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8246 (p0) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 0.1236 time to fit residues: 13.5911 Evaluate side-chains 76 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1252 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 60 optimal weight: 0.0050 chunk 1 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.0870 overall best weight: 0.6776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 341 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1297 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.120592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069111 restraints weight = 25256.591| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.84 r_work: 0.2835 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12807 Z= 0.117 Angle : 0.532 8.831 17844 Z= 0.284 Chirality : 0.041 0.396 2055 Planarity : 0.003 0.048 1798 Dihedral : 19.764 175.643 3074 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 13.52 % Favored : 84.57 % 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: -0.03 (0.24), residues: 1156 helix: 0.85 (0.22), residues: 547 sheet: -1.11 (0.49), residues: 104 loop : -0.66 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 629 TYR 0.015 0.001 TYR A1242 PHE 0.028 0.001 PHE A 518 TRP 0.008 0.001 TRP A 476 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (12807) covalent geometry : angle 0.53171 / 0.28 (17844) hydrogen bonds : bond 0.03958 / 2.70 ( 529) hydrogen bonds : angle 4.28251 / 3.04 ( 1434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: A 390 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8791 (mm) REVERT: A 511 HIS cc_start: 0.8391 (m90) cc_final: 0.7987 (m-70) REVERT: A 649 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8918 (mmmm) REVERT: A 652 LYS cc_start: 0.8754 (ptmt) cc_final: 0.8235 (pttp) REVERT: A 654 ARG cc_start: 0.8416 (tpp-160) cc_final: 0.7985 (tpp-160) REVERT: A 662 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7662 (pp) REVERT: A 933 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6307 (mp10) REVERT: A 1071 GLU cc_start: 0.8363 (tp30) cc_final: 0.7905 (tp30) REVERT: A 1148 LYS cc_start: 0.9052 (mptt) cc_final: 0.8246 (mmmt) outliers start: 20 outliers final: 13 residues processed: 75 average time/residue: 0.1318 time to fit residues: 14.1664 Evaluate side-chains 76 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 0.0170 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 44 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 930 HIS ** 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 = 0.3927 r_free = 0.3927 target = 0.120548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069071 restraints weight = 25315.344| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.84 r_work: 0.2839 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 12807 Z= 0.183 Angle : 0.779 59.108 17844 Z= 0.453 Chirality : 0.042 0.444 2055 Planarity : 0.003 0.048 1798 Dihedral : 19.762 175.611 3074 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.71 % Allowed : 13.71 % Favored : 84.57 % Cbeta Deviations : 0.09 % 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: -0.03 (0.24), residues: 1156 helix: 0.85 (0.22), residues: 547 sheet: -1.10 (0.49), residues: 104 loop : -0.66 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.013 0.001 TYR A 155 PHE 0.028 0.001 PHE A 518 TRP 0.008 0.001 TRP A 476 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (12807) covalent geometry : angle 0.77903 / 0.45 (17844) hydrogen bonds : bond 0.03952 / 2.70 ( 529) hydrogen bonds : angle 4.28348 / 3.04 ( 1434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: A 390 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8790 (mm) REVERT: A 511 HIS cc_start: 0.8397 (m90) cc_final: 0.7989 (m-70) REVERT: A 637 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9269 (mmmm) REVERT: A 649 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8920 (mmmm) REVERT: A 652 LYS cc_start: 0.8755 (ptmt) cc_final: 0.8235 (pttp) REVERT: A 654 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.7985 (tpp-160) REVERT: A 662 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7679 (pp) REVERT: A 933 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6309 (mp10) REVERT: A 1071 GLU cc_start: 0.8357 (tp30) cc_final: 0.7901 (tp30) REVERT: A 1148 LYS cc_start: 0.9054 (mptt) cc_final: 0.8248 (mmmt) outliers start: 18 outliers final: 13 residues processed: 73 average time/residue: 0.1100 time to fit residues: 11.5038 Evaluate side-chains 75 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 930 HIS ** 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 = 0.3927 r_free = 0.3927 target = 0.120549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069040 restraints weight = 24957.286| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.84 r_work: 0.2836 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 12807 Z= 0.182 Angle : 0.779 59.200 17844 Z= 0.453 Chirality : 0.042 0.446 2055 Planarity : 0.003 0.048 1798 Dihedral : 19.762 175.611 3074 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.62 % Allowed : 13.71 % Favored : 84.67 % Cbeta Deviations : 0.09 % 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: -0.03 (0.24), residues: 1156 helix: 0.85 (0.22), residues: 547 sheet: -1.10 (0.49), residues: 104 loop : -0.66 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.013 0.001 TYR A 155 PHE 0.028 0.001 PHE A 518 TRP 0.008 0.001 TRP A 476 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12807) covalent geometry : angle 0.77916 / 0.45 (17844) hydrogen bonds : bond 0.03952 / 2.70 ( 529) hydrogen bonds : angle 4.28346 / 3.04 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.17 seconds wall clock time: 53 minutes 59.40 seconds (3239.40 seconds total)