Starting phenix.real_space_refine on Thu Jul 2 18:54:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wf9_37487/07_2026/8wf9_37487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wf9_37487/07_2026/8wf9_37487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wf9_37487/07_2026/8wf9_37487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wf9_37487/07_2026/8wf9_37487.map" model { file = "/net/cci-nas-00/data/ceres_data/8wf9_37487/07_2026/8wf9_37487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wf9_37487/07_2026/8wf9_37487.cif" } resolution = 3.13 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= 0.038 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: 6 Type Number sf(0) Gaussians P 72 5.49 5 Mg 1 5.21 5 S 42 5.16 5 C 5961 2.51 5 N 1697 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 9816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 8276 Classifications: {'peptide': 1002} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 969} Chain breaks: 10 Chain: "B" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1148 Classifications: {'RNA': 54} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 47} Chain: "C" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 391 Classifications: {'RNA': 18} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.25 Number of scatterers: 9816 At special positions: 0 Unit cell: (101.26, 104.58, 127.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 72 15.00 Mg 1 11.99 O 2043 8.00 N 1697 7.00 C 5961 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: 1.06 Conformation dependent library (CDL) restraints added in 341.9 milliseconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 65.5% alpha, 7.6% beta 30 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 10 through 36 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.521A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 63 " --> pdb=" O TYR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 84 through 97 removed outlier: 4.488A pdb=" N ILE A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.637A pdb=" N VAL A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.851A pdb=" N PHE A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 removed outlier: 4.010A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.541A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.810A pdb=" N LYS A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 518 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 537 through 546 Processing helix chain 'A' and resid 552 through 577 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.077A pdb=" N PHE A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.805A pdb=" N VAL A 675 " --> pdb=" O PHE A 671 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 676' Processing helix chain 'A' and resid 683 through 708 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.577A pdb=" N LEU A 760 " --> pdb=" O HIS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 764 Processing helix chain 'A' and resid 767 through 771 removed outlier: 4.026A pdb=" N ALA A 771 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.549A pdb=" N ALA A 778 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 821 through 831 Processing helix chain 'A' and resid 831 through 849 Processing helix chain 'A' and resid 858 through 904 removed outlier: 3.714A pdb=" N VAL A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 956 through 963 removed outlier: 3.537A pdb=" N VAL A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 975 Processing helix chain 'A' and resid 981 through 1013 Proline residue: A 996 - end of helix Processing helix chain 'A' and resid 1014 through 1022 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1042 through 1058 Processing helix chain 'A' and resid 1074 through 1087 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 190 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283 removed outlier: 5.713A pdb=" N MET A 930 " --> pdb=" O GLY A 949 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 949 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 389 removed outlier: 4.256A pdb=" N GLY A 360 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A 388 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN A 358 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 414 removed outlier: 4.093A pdb=" N LYS A 361 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU A 447 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N ASN A 358 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 15.981A pdb=" N LYS A 445 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 464 removed outlier: 3.710A pdb=" N VAL A 462 " --> pdb=" O VAL A 470 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1581 1.32 - 1.45: 3009 1.45 - 1.57: 5333 1.57 - 1.69: 146 1.69 - 1.82: 78 Bond restraints: 10147 Sorted by residual: bond pdb=" CA ALA A 485 " pdb=" CB ALA A 485 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.11e+01 bond pdb=" CA PRO A 484 " pdb=" CB PRO A 484 " ideal model delta sigma weight residual 1.534 1.485 0.049 1.52e-02 4.33e+03 1.04e+01 bond pdb=" C ASP A 890 " pdb=" O ASP A 890 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.17e-02 7.31e+03 9.77e+00 bond pdb=" N9 A B 29 " pdb=" C4 A B 29 " ideal model delta sigma weight residual 1.374 1.393 -0.019 6.00e-03 2.78e+04 9.76e+00 bond pdb=" CA SER A 475 " pdb=" CB SER A 475 " ideal model delta sigma weight residual 1.528 1.482 0.047 1.56e-02 4.11e+03 8.96e+00 ... (remaining 10142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 13110 3.35 - 6.70: 775 6.70 - 10.04: 87 10.04 - 13.39: 10 13.39 - 16.74: 3 Bond angle restraints: 13985 Sorted by residual: angle pdb=" C3' G B 10 " pdb=" C2' G B 10 " pdb=" O2' G B 10 " ideal model delta sigma weight residual 110.70 125.05 -14.35 1.50e+00 4.44e-01 9.16e+01 angle pdb=" CA ARG A 835 " pdb=" CB ARG A 835 " pdb=" CG ARG A 835 " ideal model delta sigma weight residual 114.10 129.74 -15.64 2.00e+00 2.50e-01 6.12e+01 angle pdb=" O3' A B 29 " pdb=" P U B 30 " pdb=" O5' U B 30 " ideal model delta sigma weight residual 104.00 92.40 11.60 1.50e+00 4.44e-01 5.98e+01 angle pdb=" CG MET A 763 " pdb=" SD MET A 763 " pdb=" CE MET A 763 " ideal model delta sigma weight residual 100.90 117.64 -16.74 2.20e+00 2.07e-01 5.79e+01 angle pdb=" CA PHE A 671 " pdb=" CB PHE A 671 " pdb=" CG PHE A 671 " ideal model delta sigma weight residual 113.80 121.22 -7.42 1.00e+00 1.00e+00 5.50e+01 ... (remaining 13980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5519 17.43 - 34.85: 516 34.85 - 52.28: 145 52.28 - 69.71: 113 69.71 - 87.13: 24 Dihedral angle restraints: 6317 sinusoidal: 3357 harmonic: 2960 Sorted by residual: dihedral pdb=" C5' G B 21 " pdb=" C4' G B 21 " pdb=" C3' G B 21 " pdb=" O3' G B 21 " ideal model delta sinusoidal sigma weight residual 147.00 100.10 46.90 1 8.00e+00 1.56e-02 4.75e+01 dihedral pdb=" C LYS A 782 " pdb=" N LYS A 782 " pdb=" CA LYS A 782 " pdb=" CB LYS A 782 " ideal model delta harmonic sigma weight residual -122.60 -139.70 17.10 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" O4' G B 21 " pdb=" C4' G B 21 " pdb=" C3' G B 21 " pdb=" C2' G B 21 " ideal model delta sinusoidal sigma weight residual 24.00 -21.91 45.91 1 8.00e+00 1.56e-02 4.56e+01 ... (remaining 6314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1260 0.121 - 0.242: 292 0.242 - 0.362: 14 0.362 - 0.483: 4 0.483 - 0.604: 4 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA LYS A 782 " pdb=" N LYS A 782 " pdb=" C LYS A 782 " pdb=" CB LYS A 782 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" P U C 1 " pdb=" OP1 U C 1 " pdb=" OP2 U C 1 " pdb=" O5' U C 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" P U B -17 " pdb=" OP1 U B -17 " pdb=" OP2 U B -17 " pdb=" O5' U B -17 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.11e+00 ... (remaining 1571 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 30 " -0.063 2.00e-02 2.50e+03 3.34e-02 2.51e+01 pdb=" N1 U B 30 " 0.062 2.00e-02 2.50e+03 pdb=" C2 U B 30 " 0.014 2.00e-02 2.50e+03 pdb=" O2 U B 30 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U B 30 " 0.021 2.00e-02 2.50e+03 pdb=" C4 U B 30 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U B 30 " -0.029 2.00e-02 2.50e+03 pdb=" C5 U B 30 " -0.010 2.00e-02 2.50e+03 pdb=" C6 U B 30 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 19 " -0.054 2.00e-02 2.50e+03 3.20e-02 2.31e+01 pdb=" N1 U B 19 " 0.067 2.00e-02 2.50e+03 pdb=" C2 U B 19 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U B 19 " -0.013 2.00e-02 2.50e+03 pdb=" N3 U B 19 " 0.014 2.00e-02 2.50e+03 pdb=" C4 U B 19 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 19 " -0.022 2.00e-02 2.50e+03 pdb=" C5 U B 19 " -0.024 2.00e-02 2.50e+03 pdb=" C6 U B 19 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 8 " -0.055 2.00e-02 2.50e+03 2.79e-02 2.14e+01 pdb=" N9 A B 8 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A B 8 " 0.015 2.00e-02 2.50e+03 pdb=" N7 A B 8 " 0.032 2.00e-02 2.50e+03 pdb=" C5 A B 8 " -0.020 2.00e-02 2.50e+03 pdb=" C6 A B 8 " -0.029 2.00e-02 2.50e+03 pdb=" N6 A B 8 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A B 8 " -0.013 2.00e-02 2.50e+03 pdb=" C2 A B 8 " 0.030 2.00e-02 2.50e+03 pdb=" N3 A B 8 " 0.023 2.00e-02 2.50e+03 pdb=" C4 A B 8 " -0.009 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 232 2.68 - 3.24: 8897 3.24 - 3.79: 15710 3.79 - 4.35: 21986 4.35 - 4.90: 33177 Nonbonded interactions: 80002 Sorted by model distance: nonbonded pdb=" OE1 GLN A 747 " pdb="MG MG A1101 " model vdw 2.129 2.170 nonbonded pdb=" OD2 ASP A 345 " pdb=" OH TYR A 439 " model vdw 2.135 3.040 nonbonded pdb=" OG SER A 259 " pdb=" OE1 GLU A 261 " model vdw 2.199 3.040 nonbonded pdb=" OP1 G B 23 " pdb="MG MG A1101 " model vdw 2.205 2.170 nonbonded pdb=" O2' U B 18 " pdb=" OP2 G B 21 " model vdw 2.290 3.040 ... (remaining 79997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 : 0.010 0.069 10147 Z= 0.607 Angle : 1.784 16.739 13985 Z= 1.150 Chirality : 0.098 0.604 1574 Planarity : 0.007 0.071 1530 Dihedral : 17.420 87.133 4395 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.53 % Favored : 98.37 % Rotamer: Outliers : 3.07 % Allowed : 5.93 % Favored : 91.00 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 6.45 % 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: -1.03 (0.24), residues: 980 helix: -1.10 (0.17), residues: 568 sheet: 0.39 (0.82), residues: 44 loop : 0.26 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.004 ARG A 835 TYR 0.051 0.007 TYR A 343 PHE 0.041 0.006 PHE A 355 TRP 0.029 0.006 TRP A 829 HIS 0.013 0.003 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00966 / 0.61 (10147) covalent geometry : angle 1.78426 / 1.15 (13985) hydrogen bonds : bond 0.18634 / 11.99 ( 551) hydrogen bonds : angle 6.77911 / 4.76 ( 1475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.344 Fit side-chains REVERT: A 1 MET cc_start: 0.7281 (ttp) cc_final: 0.7028 (tmm) REVERT: A 10 GLN cc_start: 0.7764 (mm110) cc_final: 0.7319 (mp10) REVERT: A 96 TYR cc_start: 0.8132 (t80) cc_final: 0.7847 (t80) REVERT: A 132 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7934 (m-40) REVERT: A 139 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: A 171 ASN cc_start: 0.7025 (t0) cc_final: 0.6565 (m-40) REVERT: A 176 TYR cc_start: 0.7238 (m-80) cc_final: 0.6939 (m-80) REVERT: A 186 ASP cc_start: 0.7538 (m-30) cc_final: 0.7296 (t70) REVERT: A 187 LYS cc_start: 0.7004 (mttt) cc_final: 0.6600 (mmtp) REVERT: A 262 ARG cc_start: 0.6148 (ttt180) cc_final: 0.5873 (ttm170) REVERT: A 365 LEU cc_start: 0.6662 (tt) cc_final: 0.6237 (tp) REVERT: A 393 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6462 (tp30) REVERT: A 453 LYS cc_start: 0.8076 (mttt) cc_final: 0.7762 (tptt) REVERT: A 516 MET cc_start: 0.7109 (mtp) cc_final: 0.6742 (mtp) REVERT: A 519 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6234 (mp0) REVERT: A 520 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5235 (tm-30) REVERT: A 534 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 547 ASN cc_start: 0.7860 (m-40) cc_final: 0.7502 (m110) REVERT: A 730 LYS cc_start: 0.7441 (tttt) cc_final: 0.6593 (ptpt) REVERT: A 738 GLU cc_start: 0.7600 (pt0) cc_final: 0.7206 (pt0) REVERT: A 927 SER cc_start: 0.7705 (t) cc_final: 0.7275 (m) REVERT: A 965 LYS cc_start: 0.8433 (mttt) cc_final: 0.8210 (tttt) REVERT: A 1008 TRP cc_start: 0.7689 (t60) cc_final: 0.7371 (t60) REVERT: A 1013 TYR cc_start: 0.8567 (m-80) cc_final: 0.7642 (m-10) REVERT: A 1027 ASP cc_start: 0.8125 (t0) cc_final: 0.7847 (t0) REVERT: A 1038 ASN cc_start: 0.8421 (m-40) cc_final: 0.7752 (t0) REVERT: A 1047 ASP cc_start: 0.8068 (m-30) cc_final: 0.7739 (t0) REVERT: A 1061 TYR cc_start: 0.8775 (m-80) cc_final: 0.8377 (m-80) REVERT: A 1077 MET cc_start: 0.7705 (mmm) cc_final: 0.7296 (mmt) outliers start: 28 outliers final: 12 residues processed: 216 average time/residue: 0.1217 time to fit residues: 35.1340 Evaluate side-chains 137 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1020 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 40.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 153 GLN A 171 ASN A 219 GLN A 358 ASN A 387 ASN A 514 GLN A 517 GLN A 722 ASN A 794 GLN A 852 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.200392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148254 restraints weight = 11473.920| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.52 r_work: 0.3343 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10147 Z= 0.183 Angle : 0.604 6.229 13985 Z= 0.338 Chirality : 0.042 0.225 1574 Planarity : 0.004 0.035 1530 Dihedral : 16.909 85.625 2267 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.95 % Allowed : 8.78 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.23 (0.26), residues: 980 helix: 1.36 (0.20), residues: 574 sheet: -0.00 (0.80), residues: 44 loop : 0.19 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 885 TYR 0.018 0.002 TYR A 17 PHE 0.018 0.002 PHE A 792 TRP 0.015 0.002 TRP A 724 HIS 0.004 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (10147) covalent geometry : angle 0.60410 / 0.34 (13985) hydrogen bonds : bond 0.06919 / 4.52 ( 551) hydrogen bonds : angle 4.43386 / 3.17 ( 1475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.333 Fit side-chains REVERT: A 96 TYR cc_start: 0.8071 (t80) cc_final: 0.7825 (t80) REVERT: A 129 ASP cc_start: 0.8117 (m-30) cc_final: 0.7844 (m-30) REVERT: A 171 ASN cc_start: 0.8001 (t0) cc_final: 0.7466 (m110) REVERT: A 186 ASP cc_start: 0.7665 (m-30) cc_final: 0.7416 (m-30) REVERT: A 219 GLN cc_start: 0.8038 (mm110) cc_final: 0.7800 (mm110) REVERT: A 297 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: A 365 LEU cc_start: 0.6818 (tt) cc_final: 0.6574 (tp) REVERT: A 453 LYS cc_start: 0.8536 (mttt) cc_final: 0.8245 (mtmm) REVERT: A 520 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5583 (tm-30) REVERT: A 534 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 1013 TYR cc_start: 0.8702 (m-80) cc_final: 0.8174 (m-10) REVERT: A 1038 ASN cc_start: 0.8423 (m-40) cc_final: 0.7927 (t0) REVERT: A 1077 MET cc_start: 0.8405 (mmm) cc_final: 0.8190 (mmt) outliers start: 36 outliers final: 19 residues processed: 152 average time/residue: 0.1126 time to fit residues: 23.4963 Evaluate side-chains 123 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 0.0010 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.197188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144067 restraints weight = 11499.630| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.57 r_work: 0.3298 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 10147 Z= 0.181 Angle : 0.539 6.538 13985 Z= 0.298 Chirality : 0.040 0.229 1574 Planarity : 0.004 0.036 1530 Dihedral : 16.618 79.535 2251 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.96 % Allowed : 10.21 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.75 (0.27), residues: 980 helix: 1.90 (0.21), residues: 577 sheet: 0.05 (0.81), residues: 46 loop : 0.19 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 105 TYR 0.018 0.002 TYR A 17 PHE 0.018 0.002 PHE A 792 TRP 0.010 0.002 TRP A1008 HIS 0.005 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (10147) covalent geometry : angle 0.53895 / 0.30 (13985) hydrogen bonds : bond 0.05781 / 3.78 ( 551) hydrogen bonds : angle 4.18481 / 3.02 ( 1475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.292 Fit side-chains REVERT: A 96 TYR cc_start: 0.8121 (t80) cc_final: 0.7861 (t80) REVERT: A 129 ASP cc_start: 0.8050 (m-30) cc_final: 0.7822 (m-30) REVERT: A 186 ASP cc_start: 0.7706 (m-30) cc_final: 0.7352 (m-30) REVERT: A 297 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: A 453 LYS cc_start: 0.8578 (mttt) cc_final: 0.8282 (mtmm) REVERT: A 520 GLU cc_start: 0.6469 (mt-10) cc_final: 0.5556 (tm-30) REVERT: A 781 MET cc_start: 0.7453 (ttp) cc_final: 0.7054 (ttt) REVERT: A 816 GLN cc_start: 0.7886 (tt0) cc_final: 0.7651 (tp40) REVERT: A 922 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7982 (mp0) REVERT: A 1013 TYR cc_start: 0.8551 (m-80) cc_final: 0.8016 (m-10) REVERT: A 1038 ASN cc_start: 0.8295 (m-40) cc_final: 0.7825 (t0) outliers start: 27 outliers final: 19 residues processed: 126 average time/residue: 0.0909 time to fit residues: 16.8105 Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 105 optimal weight: 40.0000 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 GLN A 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.199723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145568 restraints weight = 11558.880| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.74 r_work: 0.3346 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 10147 Z= 0.117 Angle : 0.455 5.299 13985 Z= 0.253 Chirality : 0.036 0.184 1574 Planarity : 0.003 0.033 1530 Dihedral : 16.551 73.998 2248 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.20 % Allowed : 11.53 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.27), residues: 980 helix: 2.19 (0.21), residues: 579 sheet: 0.33 (0.87), residues: 41 loop : 0.32 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.014 0.001 TYR A 17 PHE 0.015 0.001 PHE A 792 TRP 0.010 0.001 TRP A1008 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10147) covalent geometry : angle 0.45521 / 0.25 (13985) hydrogen bonds : bond 0.04916 / 3.24 ( 551) hydrogen bonds : angle 3.95015 / 2.85 ( 1475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.328 Fit side-chains REVERT: A 96 TYR cc_start: 0.8075 (t80) cc_final: 0.7866 (t80) REVERT: A 105 ARG cc_start: 0.6393 (ptp90) cc_final: 0.6080 (ptt-90) REVERT: A 219 GLN cc_start: 0.8211 (mm110) cc_final: 0.7977 (mm-40) REVERT: A 297 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: A 453 LYS cc_start: 0.8590 (mttt) cc_final: 0.8286 (mtmm) REVERT: A 520 GLU cc_start: 0.6329 (mt-10) cc_final: 0.5451 (tm-30) REVERT: A 763 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8177 (mtm) REVERT: A 781 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6979 (ttt) REVERT: A 816 GLN cc_start: 0.7859 (tt0) cc_final: 0.7648 (tp40) REVERT: A 922 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8044 (mp0) REVERT: A 1013 TYR cc_start: 0.8518 (m-80) cc_final: 0.8096 (m-10) REVERT: A 1038 ASN cc_start: 0.8235 (m-40) cc_final: 0.7776 (t0) outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 0.1130 time to fit residues: 19.5541 Evaluate side-chains 116 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 HIS A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.197349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140964 restraints weight = 11306.569| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.67 r_work: 0.3307 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10147 Z= 0.146 Angle : 0.477 6.591 13985 Z= 0.259 Chirality : 0.038 0.187 1574 Planarity : 0.004 0.044 1530 Dihedral : 16.458 74.055 2244 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.74 % Allowed : 11.96 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.27), residues: 980 helix: 2.23 (0.21), residues: 579 sheet: 0.12 (0.88), residues: 41 loop : 0.34 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 128 TYR 0.015 0.002 TYR A 17 PHE 0.019 0.001 PHE A 792 TRP 0.012 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10147) covalent geometry : angle 0.47667 / 0.26 (13985) hydrogen bonds : bond 0.04868 / 3.18 ( 551) hydrogen bonds : angle 3.92939 / 2.84 ( 1475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.330 Fit side-chains REVERT: A 94 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7611 (ttp80) REVERT: A 105 ARG cc_start: 0.6463 (ptp90) cc_final: 0.6065 (ptt-90) REVERT: A 297 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: A 453 LYS cc_start: 0.8629 (mttt) cc_final: 0.8342 (mtmt) REVERT: A 520 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5474 (tm-30) REVERT: A 763 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: A 781 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6985 (ttt) REVERT: A 816 GLN cc_start: 0.7946 (tt0) cc_final: 0.7704 (tp40) REVERT: A 1013 TYR cc_start: 0.8497 (m-80) cc_final: 0.7902 (m-80) REVERT: A 1038 ASN cc_start: 0.8168 (m-40) cc_final: 0.7754 (t0) outliers start: 25 outliers final: 18 residues processed: 122 average time/residue: 0.1041 time to fit residues: 17.9392 Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 0.0370 chunk 97 optimal weight: 0.0570 chunk 72 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.199950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145904 restraints weight = 11580.122| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.52 r_work: 0.3349 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10147 Z= 0.106 Angle : 0.435 5.486 13985 Z= 0.239 Chirality : 0.035 0.161 1574 Planarity : 0.003 0.037 1530 Dihedral : 16.447 73.969 2244 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.85 % Allowed : 12.07 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 980 helix: 2.37 (0.21), residues: 578 sheet: 0.30 (0.89), residues: 41 loop : 0.41 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.013 0.001 TYR A 17 PHE 0.015 0.001 PHE A 792 TRP 0.013 0.001 TRP A1008 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (10147) covalent geometry : angle 0.43521 / 0.24 (13985) hydrogen bonds : bond 0.04450 / 2.93 ( 551) hydrogen bonds : angle 3.80606 / 2.75 ( 1475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.6528 (ptp90) cc_final: 0.6162 (ptt-90) REVERT: A 297 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: A 393 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: A 453 LYS cc_start: 0.8611 (mttt) cc_final: 0.8270 (mtmm) REVERT: A 520 GLU cc_start: 0.6352 (mt-10) cc_final: 0.5491 (tm-30) REVERT: A 763 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8216 (mtm) REVERT: A 781 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6970 (ttt) REVERT: A 831 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6929 (mt-10) REVERT: A 1013 TYR cc_start: 0.8445 (m-80) cc_final: 0.7805 (m-80) REVERT: A 1038 ASN cc_start: 0.8113 (m-40) cc_final: 0.7746 (t0) outliers start: 26 outliers final: 16 residues processed: 126 average time/residue: 0.0951 time to fit residues: 17.3309 Evaluate side-chains 122 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 HIS A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.197800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143862 restraints weight = 11466.217| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.53 r_work: 0.3312 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10147 Z= 0.141 Angle : 0.469 7.178 13985 Z= 0.253 Chirality : 0.037 0.172 1574 Planarity : 0.004 0.033 1530 Dihedral : 16.388 74.001 2244 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.63 % Allowed : 12.51 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.27), residues: 980 helix: 2.36 (0.21), residues: 578 sheet: 0.21 (0.85), residues: 43 loop : 0.45 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.014 0.001 TYR A 17 PHE 0.032 0.001 PHE A 513 TRP 0.014 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10147) covalent geometry : angle 0.46946 / 0.25 (13985) hydrogen bonds : bond 0.04596 / 3.01 ( 551) hydrogen bonds : angle 3.85263 / 2.80 ( 1475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.344 Fit side-chains REVERT: A 20 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8621 (ttt) REVERT: A 94 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7616 (ttp80) REVERT: A 105 ARG cc_start: 0.6618 (ptp90) cc_final: 0.6088 (ptt-90) REVERT: A 297 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: A 453 LYS cc_start: 0.8599 (mttt) cc_final: 0.8341 (mtmt) REVERT: A 520 GLU cc_start: 0.6393 (mt-10) cc_final: 0.5525 (tm-30) REVERT: A 763 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: A 781 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7173 (ttt) REVERT: A 831 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6954 (mt-10) REVERT: A 937 GLU cc_start: 0.7580 (tt0) cc_final: 0.7343 (tt0) REVERT: A 1013 TYR cc_start: 0.8436 (m-80) cc_final: 0.7965 (m-80) REVERT: A 1038 ASN cc_start: 0.8089 (m-40) cc_final: 0.7647 (t0) REVERT: A 1077 MET cc_start: 0.8197 (mmt) cc_final: 0.7911 (mmt) outliers start: 24 outliers final: 18 residues processed: 124 average time/residue: 0.1024 time to fit residues: 17.9606 Evaluate side-chains 124 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 105 optimal weight: 40.0000 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 HIS A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.196009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141489 restraints weight = 11476.224| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.59 r_work: 0.3282 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10147 Z= 0.179 Angle : 0.505 6.778 13985 Z= 0.270 Chirality : 0.038 0.187 1574 Planarity : 0.004 0.035 1530 Dihedral : 16.373 74.157 2241 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.07 % Allowed : 12.18 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.27), residues: 980 helix: 2.29 (0.21), residues: 576 sheet: -0.20 (0.82), residues: 43 loop : 0.42 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 800 TYR 0.015 0.002 TYR A 736 PHE 0.039 0.002 PHE A 513 TRP 0.017 0.002 TRP A1008 HIS 0.004 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (10147) covalent geometry : angle 0.50481 / 0.27 (13985) hydrogen bonds : bond 0.04792 / 3.14 ( 551) hydrogen bonds : angle 3.90574 / 2.84 ( 1475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8644 (ttt) REVERT: A 94 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7578 (ttp80) REVERT: A 105 ARG cc_start: 0.6627 (ptp90) cc_final: 0.6062 (ptt-90) REVERT: A 297 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: A 398 MET cc_start: 0.8062 (tpp) cc_final: 0.7661 (mmm) REVERT: A 453 LYS cc_start: 0.8693 (mttt) cc_final: 0.8204 (mtmm) REVERT: A 520 GLU cc_start: 0.6496 (mt-10) cc_final: 0.5643 (tm-30) REVERT: A 763 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8254 (mtm) REVERT: A 831 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6975 (mt-10) REVERT: A 937 GLU cc_start: 0.7640 (tt0) cc_final: 0.7388 (tt0) REVERT: A 1013 TYR cc_start: 0.8412 (m-80) cc_final: 0.8064 (m-10) REVERT: A 1038 ASN cc_start: 0.8075 (m-40) cc_final: 0.7624 (t0) outliers start: 28 outliers final: 17 residues processed: 124 average time/residue: 0.1011 time to fit residues: 17.5370 Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 985 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.196262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142620 restraints weight = 11424.133| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.45 r_work: 0.3308 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10147 Z= 0.140 Angle : 0.484 10.936 13985 Z= 0.257 Chirality : 0.036 0.177 1574 Planarity : 0.004 0.052 1530 Dihedral : 16.362 73.975 2241 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.63 % Allowed : 12.51 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.27), residues: 980 helix: 2.33 (0.21), residues: 575 sheet: -0.09 (0.83), residues: 43 loop : 0.44 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 718 TYR 0.015 0.002 TYR A 364 PHE 0.027 0.001 PHE A 513 TRP 0.016 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10147) covalent geometry : angle 0.48390 / 0.26 (13985) hydrogen bonds : bond 0.04572 / 2.99 ( 551) hydrogen bonds : angle 3.86707 / 2.81 ( 1475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.348 Fit side-chains REVERT: A 20 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8610 (ttt) REVERT: A 94 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7582 (ttp80) REVERT: A 105 ARG cc_start: 0.6683 (ptp90) cc_final: 0.6118 (ptt-90) REVERT: A 297 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: A 453 LYS cc_start: 0.8699 (mttt) cc_final: 0.8216 (mtmm) REVERT: A 520 GLU cc_start: 0.6438 (mt-10) cc_final: 0.5603 (tm-30) REVERT: A 729 MET cc_start: 0.7230 (tpp) cc_final: 0.7015 (tpp) REVERT: A 831 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6975 (mt-10) REVERT: A 937 GLU cc_start: 0.7608 (tt0) cc_final: 0.7354 (tt0) REVERT: A 1013 TYR cc_start: 0.8386 (m-80) cc_final: 0.8018 (m-10) REVERT: A 1038 ASN cc_start: 0.8039 (m-40) cc_final: 0.7618 (t0) outliers start: 24 outliers final: 19 residues processed: 117 average time/residue: 0.0988 time to fit residues: 16.3387 Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 985 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.195841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141879 restraints weight = 11229.446| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.31 r_work: 0.3305 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10147 Z= 0.137 Angle : 0.485 9.960 13985 Z= 0.257 Chirality : 0.036 0.174 1574 Planarity : 0.004 0.043 1530 Dihedral : 16.345 73.959 2241 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.52 % Allowed : 12.40 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.27), residues: 980 helix: 2.34 (0.21), residues: 577 sheet: -0.08 (0.83), residues: 43 loop : 0.36 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 718 TYR 0.026 0.002 TYR A 364 PHE 0.027 0.001 PHE A 513 TRP 0.017 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10147) covalent geometry : angle 0.48550 / 0.26 (13985) hydrogen bonds : bond 0.04523 / 2.96 ( 551) hydrogen bonds : angle 3.84752 / 2.80 ( 1475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.334 Fit side-chains REVERT: A 20 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8597 (ttt) REVERT: A 94 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7595 (ttp80) REVERT: A 105 ARG cc_start: 0.6711 (ptp90) cc_final: 0.6150 (ptt-90) REVERT: A 297 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: A 453 LYS cc_start: 0.8708 (mttt) cc_final: 0.8204 (mtmm) REVERT: A 520 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5614 (tm-30) REVERT: A 729 MET cc_start: 0.7215 (tpp) cc_final: 0.6995 (tpp) REVERT: A 831 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 1013 TYR cc_start: 0.8384 (m-80) cc_final: 0.8008 (m-10) REVERT: A 1038 ASN cc_start: 0.8054 (m-40) cc_final: 0.7633 (t0) outliers start: 23 outliers final: 19 residues processed: 115 average time/residue: 0.0922 time to fit residues: 15.0331 Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 985 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.4980 chunk 102 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 41 optimal weight: 0.0170 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.197137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142745 restraints weight = 11504.984| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.69 r_work: 0.3316 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10147 Z= 0.132 Angle : 0.477 9.411 13985 Z= 0.253 Chirality : 0.036 0.171 1574 Planarity : 0.004 0.041 1530 Dihedral : 16.331 73.929 2241 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.31 % Allowed : 12.84 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.27), residues: 980 helix: 2.37 (0.21), residues: 577 sheet: -0.08 (0.84), residues: 43 loop : 0.36 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 718 TYR 0.020 0.002 TYR A 364 PHE 0.025 0.001 PHE A 513 TRP 0.017 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10147) covalent geometry : angle 0.47689 / 0.25 (13985) hydrogen bonds : bond 0.04467 / 2.93 ( 551) hydrogen bonds : angle 3.82929 / 2.78 ( 1475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.53 seconds wall clock time: 43 minutes 42.97 seconds (2622.97 seconds total)