Starting phenix.real_space_refine on Fri Jul 3 05:28:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6t_41080/07_2026/8t6t_41080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6t_41080/07_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_41080/07_2026/8t6t_41080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6t_41080/07_2026/8t6t_41080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6t_41080/07_2026/8t6t_41080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6t_41080/07_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-dev-6108/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: 2.64, per 1000 atoms: 0.21 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: 1.02 Conformation dependent library (CDL) restraints added in 423.9 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: 1.17 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: 2.04 Time building geometry restraints manager: 1.37 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: 17644 5.16 - 10.32: 148 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: 3.840 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.200 Find NCS groups from input model: 0.030 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- 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= 0.372 Angle : 1.344 25.807 17844 Z= 0.933 Chirality : 0.106 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 0.00550 / 0.37 (12807) covalent geometry : angle 1.34394 / 0.93 (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 : 0.343 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: 0.1092 time to fit residues: 11.8138 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 : 0.304 ------------------------------------------------------------------------------- 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: 8.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 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 = 0.3918 r_free = 0.3918 target = 0.119460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067540 restraints weight = 25255.261| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.90 r_work: 0.2812 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0981 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= 0.195 Angle : 0.657 8.736 17844 Z= 0.363 Chirality : 0.044 0.357 2055 Planarity : 0.004 0.056 1798 Dihedral : 20.075 177.353 3076 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.71 % Allowed : 9.33 % Favored : 88.95 % 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: -0.11 (0.22), residues: 521 sheet: -1.69 (0.45), residues: 110 loop : -1.01 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 307 TYR 0.015 0.001 TYR A 362 PHE 0.009 0.001 PHE A1046 TRP 0.016 0.001 TRP A1136 HIS 0.003 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (12807) covalent geometry : angle 0.65707 / 0.36 (17844) hydrogen bonds : bond 0.05602 / 3.78 ( 529) hydrogen bonds : angle 5.04215 / 3.61 ( 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: 18 poor density : 64 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7004 (ptp) REVERT: A 652 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8455 (pptt) REVERT: A 654 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.8083 (tpp-160) REVERT: A 1148 LYS cc_start: 0.9059 (mptt) cc_final: 0.8803 (mmtm) outliers start: 18 outliers final: 11 residues processed: 76 average time/residue: 0.1159 time to fit residues: 12.5094 Evaluate side-chains 69 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3900 r_free = 0.3900 target = 0.118450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066781 restraints weight = 25443.620| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.92 r_work: 0.2781 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12807 Z= 0.201 Angle : 0.603 8.184 17844 Z= 0.332 Chirality : 0.043 0.485 2055 Planarity : 0.004 0.054 1798 Dihedral : 20.123 179.519 3074 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.10 % Allowed : 10.76 % 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: 0.20 (0.22), residues: 528 sheet: -1.45 (0.47), residues: 104 loop : -0.91 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1317 TYR 0.019 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 0.00432 / 0.20 (12807) covalent geometry : angle 0.60334 / 0.33 (17844) hydrogen bonds : bond 0.05025 / 3.43 ( 529) hydrogen bonds : angle 4.71415 / 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 82 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7045 (ptp) REVERT: A 652 LYS cc_start: 0.8689 (ptmt) cc_final: 0.8471 (pptt) REVERT: A 654 ARG cc_start: 0.8369 (tpp-160) cc_final: 0.8109 (tpp-160) REVERT: A 763 MET cc_start: 0.3389 (tpt) cc_final: 0.3183 (tpt) REVERT: A 1148 LYS cc_start: 0.9002 (mptt) cc_final: 0.8206 (mmmt) outliers start: 22 outliers final: 14 residues processed: 76 average time/residue: 0.1123 time to fit residues: 12.6556 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 : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL 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 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: 0.5980 chunk 124 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.119825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068178 restraints weight = 25173.481| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.85 r_work: 0.2815 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12807 Z= 0.135 Angle : 0.547 8.243 17844 Z= 0.301 Chirality : 0.041 0.410 2055 Planarity : 0.003 0.053 1798 Dihedral : 20.153 176.261 3074 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 11.33 % Favored : 86.67 % 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: -0.53 (0.24), residues: 1156 helix: 0.42 (0.22), residues: 535 sheet: -1.39 (0.48), residues: 104 loop : -0.86 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1122 TYR 0.013 0.001 TYR A 155 PHE 0.015 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 0.00281 / 0.13 (12807) covalent geometry : angle 0.54715 / 0.30 (17844) hydrogen bonds : bond 0.04477 / 3.06 ( 529) hydrogen bonds : angle 4.55931 / 3.26 ( 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 84 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8743 (mm) REVERT: A 511 HIS cc_start: 0.8374 (m90) cc_final: 0.8044 (m-70) REVERT: A 649 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8932 (mmmm) REVERT: A 652 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8091 (pttp) REVERT: A 654 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8000 (tpp-160) REVERT: A 1148 LYS cc_start: 0.9019 (mptt) cc_final: 0.8706 (mmtp) outliers start: 21 outliers final: 14 residues processed: 79 average time/residue: 0.1144 time to fit residues: 13.0494 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 : 0.373 ------------------------------------------------------------------------------- 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 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 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: 0.0980 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.117147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.065004 restraints weight = 25635.441| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.96 r_work: 0.2753 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 12807 Z= 0.358 Angle : 0.663 8.555 17844 Z= 0.358 Chirality : 0.046 0.450 2055 Planarity : 0.004 0.048 1798 Dihedral : 20.100 177.714 3074 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.29 % Allowed : 11.81 % Favored : 85.90 % 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: -0.69 (0.23), residues: 1156 helix: 0.30 (0.22), residues: 545 sheet: -1.48 (0.47), residues: 104 loop : -0.97 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.024 0.002 TYR A 362 PHE 0.035 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 0.00792 / 0.36 (12807) covalent geometry : angle 0.66254 / 0.36 (17844) hydrogen bonds : bond 0.05230 / 3.58 ( 529) hydrogen bonds : angle 4.66805 / 3.35 ( 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 83 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 HIS cc_start: 0.8357 (m90) cc_final: 0.8009 (m-70) REVERT: A 649 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8912 (mmmm) REVERT: A 652 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8187 (pttp) REVERT: A 654 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.7933 (tpp-160) REVERT: A 1148 LYS cc_start: 0.9091 (mptt) cc_final: 0.8804 (mmtp) outliers start: 24 outliers final: 17 residues processed: 78 average time/residue: 0.1195 time to fit residues: 13.3327 Evaluate side-chains 74 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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: 1.9990 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A1066 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.119295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067572 restraints weight = 25288.039| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.87 r_work: 0.2798 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12807 Z= 0.143 Angle : 0.544 7.669 17844 Z= 0.298 Chirality : 0.041 0.375 2055 Planarity : 0.003 0.050 1798 Dihedral : 20.147 175.712 3074 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.90 % Allowed : 12.76 % Favored : 85.33 % 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: 0.53 (0.22), residues: 545 sheet: -1.39 (0.47), residues: 104 loop : -0.79 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1122 TYR 0.013 0.001 TYR A 155 PHE 0.020 0.001 PHE A 518 TRP 0.011 0.001 TRP A 476 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12807) covalent geometry : angle 0.54421 / 0.30 (17844) hydrogen bonds : bond 0.04448 / 3.03 ( 529) hydrogen bonds : angle 4.48672 / 3.20 ( 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 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6077 (pt0) REVERT: A 390 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 511 HIS cc_start: 0.8308 (m90) cc_final: 0.7959 (m-70) REVERT: A 649 LYS cc_start: 0.9197 (mmtm) cc_final: 0.8903 (mmmm) REVERT: A 652 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8214 (pttp) REVERT: A 654 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.7893 (tpp-160) REVERT: A 662 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7989 (pp) REVERT: A 1148 LYS cc_start: 0.9027 (mptt) cc_final: 0.8747 (mmtp) outliers start: 20 outliers final: 14 residues processed: 75 average time/residue: 0.1187 time to fit residues: 12.7300 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 : 0.422 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 390 LEU 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: 0.0040 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 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: 0.6980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN A 413 GLN A 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.119674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068013 restraints weight = 25065.358| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.87 r_work: 0.2809 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12807 Z= 0.142 Angle : 0.535 9.692 17844 Z= 0.292 Chirality : 0.041 0.378 2055 Planarity : 0.003 0.049 1798 Dihedral : 20.043 176.512 3074 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.19 % Allowed : 13.05 % Favored : 84.76 % 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: -0.21 (0.24), residues: 1156 helix: 0.67 (0.22), residues: 545 sheet: -1.29 (0.48), residues: 104 loop : -0.68 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.015 0.001 TYR A 155 PHE 0.033 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 0.00298 / 0.14 (12807) covalent geometry : angle 0.53467 / 0.29 (17844) hydrogen bonds : bond 0.04221 / 2.87 ( 529) hydrogen bonds : angle 4.38137 / 3.12 ( 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 84 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.5970 (pt0) REVERT: A 390 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 511 HIS cc_start: 0.8313 (m90) cc_final: 0.7934 (m-70) REVERT: A 629 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8733 (mmt-90) REVERT: A 649 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8926 (mmmm) REVERT: A 652 LYS cc_start: 0.8761 (ptmt) cc_final: 0.8260 (pttp) REVERT: A 654 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.7964 (tpp-160) REVERT: A 662 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7780 (pp) outliers start: 23 outliers final: 15 residues processed: 79 average time/residue: 0.1058 time to fit residues: 12.0434 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 : 0.302 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065842 restraints weight = 25148.768| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.85 r_work: 0.2762 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12807 Z= 0.272 Angle : 0.615 8.631 17844 Z= 0.330 Chirality : 0.044 0.433 2055 Planarity : 0.004 0.046 1798 Dihedral : 20.025 173.243 3074 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 13.71 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1156 helix: 0.62 (0.22), residues: 546 sheet: -1.34 (0.47), residues: 104 loop : -0.81 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.019 0.001 TYR A 362 PHE 0.009 0.001 PHE A 98 TRP 0.011 0.001 TRP A 476 HIS 0.007 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 (12807) covalent geometry : angle 0.61515 / 0.33 (17844) hydrogen bonds : bond 0.04751 / 3.24 ( 529) hydrogen bonds : angle 4.48060 / 3.21 ( 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 82 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6008 (pt0) REVERT: A 390 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8800 (mm) REVERT: A 511 HIS cc_start: 0.8319 (m90) cc_final: 0.7925 (m-70) REVERT: A 649 LYS cc_start: 0.9201 (mmtm) cc_final: 0.8924 (mmmm) REVERT: A 652 LYS cc_start: 0.8808 (ptmt) cc_final: 0.8281 (pttp) REVERT: A 654 ARG cc_start: 0.8352 (tpp-160) cc_final: 0.7882 (tpp-160) REVERT: A 662 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7772 (pp) REVERT: A 1148 LYS cc_start: 0.9066 (mptt) cc_final: 0.8752 (mmtp) REVERT: A 1303 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8345 (ttm170) outliers start: 21 outliers final: 15 residues processed: 77 average time/residue: 0.1219 time to fit residues: 13.4567 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 : 0.384 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 80 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** A1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.119430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.067815 restraints weight = 25269.309| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.82 r_work: 0.2805 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12807 Z= 0.140 Angle : 0.551 8.550 17844 Z= 0.295 Chirality : 0.041 0.391 2055 Planarity : 0.003 0.048 1798 Dihedral : 20.021 176.860 3074 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.71 % Allowed : 14.19 % Favored : 84.10 % 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: -0.15 (0.24), residues: 1156 helix: 0.76 (0.22), residues: 547 sheet: -1.25 (0.48), residues: 104 loop : -0.71 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.015 0.001 TYR A1242 PHE 0.031 0.001 PHE A 518 TRP 0.011 0.001 TRP A 476 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (12807) covalent geometry : angle 0.55118 / 0.30 (17844) hydrogen bonds : bond 0.04220 / 2.87 ( 529) hydrogen bonds : angle 4.37718 / 3.12 ( 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 76 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6002 (pt0) REVERT: A 390 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 511 HIS cc_start: 0.8328 (m90) cc_final: 0.7924 (m-70) REVERT: A 629 ARG cc_start: 0.8936 (mmt-90) cc_final: 0.8728 (mmt-90) REVERT: A 649 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8922 (mmmm) REVERT: A 652 LYS cc_start: 0.8790 (ptmt) cc_final: 0.8276 (pttp) REVERT: A 654 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.7954 (tpp-160) REVERT: A 662 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7600 (pp) REVERT: A 667 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7852 (mm) outliers start: 18 outliers final: 13 residues processed: 70 average time/residue: 0.1180 time to fit residues: 11.8558 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 : 0.354 ------------------------------------------------------------------------------- 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 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 667 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** 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 = 0.3901 r_free = 0.3901 target = 0.118788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.067064 restraints weight = 25336.341| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.84 r_work: 0.2790 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12807 Z= 0.180 Angle : 0.576 9.865 17844 Z= 0.305 Chirality : 0.042 0.414 2055 Planarity : 0.003 0.047 1798 Dihedral : 19.936 175.376 3074 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.81 % Allowed : 14.00 % Favored : 84.19 % 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: 0.77 (0.22), residues: 547 sheet: -1.23 (0.49), residues: 104 loop : -0.72 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.015 0.001 TYR A 155 PHE 0.028 0.001 PHE A 518 TRP 0.010 0.001 TRP A 476 HIS 0.005 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (12807) covalent geometry : angle 0.57612 / 0.31 (17844) hydrogen bonds : bond 0.04340 / 2.96 ( 529) hydrogen bonds : angle 4.37625 / 3.12 ( 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 78 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6005 (pt0) REVERT: A 390 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8784 (mm) REVERT: A 511 HIS cc_start: 0.8320 (m90) cc_final: 0.7910 (m-70) REVERT: A 637 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9263 (mmmm) REVERT: A 649 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8859 (mmtm) REVERT: A 652 LYS cc_start: 0.8790 (ptmt) cc_final: 0.8336 (pttp) REVERT: A 654 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.7927 (tpp-160) REVERT: A 662 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7626 (pp) REVERT: A 1252 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8252 (p0) outliers start: 19 outliers final: 13 residues processed: 73 average time/residue: 0.1038 time to fit residues: 10.8663 Evaluate side-chains 74 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1252 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3894 r_free = 0.3894 target = 0.118380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066339 restraints weight = 25099.569| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.91 r_work: 0.2772 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12807 Z= 0.216 Angle : 0.593 11.286 17844 Z= 0.314 Chirality : 0.043 0.428 2055 Planarity : 0.003 0.047 1798 Dihedral : 19.922 174.953 3074 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.71 % Allowed : 13.90 % Favored : 84.38 % 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: -0.21 (0.24), residues: 1156 helix: 0.71 (0.22), residues: 554 sheet: -1.27 (0.49), residues: 104 loop : -0.77 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.016 0.001 TYR A 362 PHE 0.007 0.001 PHE A 518 TRP 0.011 0.001 TRP A 476 HIS 0.005 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (12807) covalent geometry : angle 0.59297 / 0.31 (17844) hydrogen bonds : bond 0.04434 / 3.01 ( 529) hydrogen bonds : angle 4.40696 / 3.15 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3119.31 seconds wall clock time: 54 minutes 9.13 seconds (3249.13 seconds total)