Starting phenix.real_space_refine on Wed Aug 5 12:10:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wf9_37487/08_2026/8wf9_37487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wf9_37487/08_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_37487/08_2026/8wf9_37487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wf9_37487/08_2026/8wf9_37487.map" model { file = "/net/cci-nas-00/data/ceres_data/8wf9_37487/08_2026/8wf9_37487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wf9_37487/08_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-2.2rc3-6140/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: 1.51, per 1000 atoms: 0.15 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: 0.79 Conformation dependent library (CDL) restraints added in 215.9 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: 0.86 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: 1.64 Time building geometry restraints manager: 0.94 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: 13124 3.35 - 6.70: 760 6.70 - 10.04: 88 10.04 - 13.39: 11 13.39 - 16.74: 2 Bond angle restraints: 13985 Sorted by residual: 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=" 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 angle pdb=" CB GLU A 152 " pdb=" CG GLU A 152 " pdb=" CD GLU A 152 " ideal model delta sigma weight residual 112.60 125.01 -12.41 1.70e+00 3.46e-01 5.33e+01 angle pdb=" C4' G B 21 " pdb=" O4' G B 21 " pdb=" C1' G B 21 " ideal model delta sigma weight residual 109.70 104.87 4.83 7.00e-01 2.04e+00 4.77e+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: 1291 0.121 - 0.242: 263 0.242 - 0.362: 12 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: 1.460 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.990 ------------------------------------------------------------------------------- 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= 0.620 Angle : 1.771 16.739 13985 Z= 1.146 Chirality : 0.094 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 0.00964 / 0.62 (10147) covalent geometry : angle 1.77072 / 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 : 0.333 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: 0.7318 (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: 0.6461 (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: 0.6740 (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: 0.5236 (tm-30) REVERT: A 534 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 547 ASN cc_start: 0.7860 (m-40) cc_final: 0.7503 (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 746 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.7031 (mtm110) 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: 0.7641 (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: 0.0990 time to fit residues: 28.7938 Evaluate side-chains 138 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 746 ARG 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: 50.0000 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 = 0.200384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148475 restraints weight = 11484.629| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.53 r_work: 0.3339 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10147 Z= 0.187 Angle : 0.617 5.939 13985 Z= 0.343 Chirality : 0.042 0.166 1574 Planarity : 0.004 0.035 1530 Dihedral : 16.869 85.683 2271 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.95 % Allowed : 8.67 % Favored : 87.38 % 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: 1.24 (0.26), residues: 980 helix: 1.36 (0.20), residues: 574 sheet: -0.00 (0.80), residues: 44 loop : 0.21 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 835 TYR 0.018 0.002 TYR A 886 PHE 0.018 0.002 PHE A 792 TRP 0.015 0.002 TRP A 724 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (10147) covalent geometry : angle 0.61731 / 0.34 (13985) hydrogen bonds : bond 0.07052 / 4.62 ( 551) hydrogen bonds : angle 4.45068 / 3.18 ( 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 157 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.207 Fit side-chains REVERT: A 55 MET cc_start: 0.7278 (mmm) cc_final: 0.6988 (mmm) REVERT: A 96 TYR cc_start: 0.8078 (t80) cc_final: 0.7834 (t80) REVERT: A 129 ASP cc_start: 0.8111 (m-30) cc_final: 0.7845 (m-30) REVERT: A 171 ASN cc_start: 0.8003 (t0) cc_final: 0.7465 (m110) REVERT: A 186 ASP cc_start: 0.7690 (m-30) cc_final: 0.7435 (m-30) REVERT: A 219 GLN cc_start: 0.8029 (mm110) cc_final: 0.7798 (mm110) REVERT: A 297 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 365 LEU cc_start: 0.6820 (tt) cc_final: 0.6228 (tp) REVERT: A 453 LYS cc_start: 0.8538 (mttt) cc_final: 0.8243 (mtmm) REVERT: A 520 GLU cc_start: 0.6490 (mt-10) cc_final: 0.5572 (tm-30) REVERT: A 534 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 1013 TYR cc_start: 0.8675 (m-80) cc_final: 0.8157 (m-10) REVERT: A 1038 ASN cc_start: 0.8404 (m-40) cc_final: 0.7940 (t0) REVERT: A 1077 MET cc_start: 0.8411 (mmm) cc_final: 0.8196 (mmt) outliers start: 36 outliers final: 18 residues processed: 150 average time/residue: 0.0860 time to fit residues: 17.9934 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 : 0.244 ------------------------------------------------------------------------------- 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 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: 9.9990 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: 3.9990 chunk 64 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8388 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.199920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147332 restraints weight = 11485.647| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.44 r_work: 0.3354 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 10147 Z= 0.136 Angle : 0.499 6.074 13985 Z= 0.277 Chirality : 0.038 0.211 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.528 77.764 2251 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.41 % Allowed : 10.43 % Favored : 87.16 % 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: 1.98 (0.27), residues: 980 helix: 2.10 (0.21), residues: 577 sheet: 0.25 (0.79), residues: 46 loop : 0.24 (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 0.016 0.001 PHE A 792 TRP 0.011 0.002 TRP A1008 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (10147) covalent geometry : angle 0.49919 / 0.28 (13985) hydrogen bonds : bond 0.05450 / 3.58 ( 551) hydrogen bonds : angle 4.08271 / 2.94 ( 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 138 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.251 Fit side-chains REVERT: A 1 MET cc_start: 0.8147 (ttp) cc_final: 0.7688 (tmm) REVERT: A 96 TYR cc_start: 0.8062 (t80) cc_final: 0.7822 (t80) REVERT: A 129 ASP cc_start: 0.8038 (m-30) cc_final: 0.7802 (m-30) REVERT: A 171 ASN cc_start: 0.7682 (t0) cc_final: 0.7250 (m110) REVERT: A 297 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: A 365 LEU cc_start: 0.6794 (tt) cc_final: 0.6259 (tp) REVERT: A 453 LYS cc_start: 0.8512 (mttt) cc_final: 0.8226 (mtmm) REVERT: A 520 GLU cc_start: 0.6436 (mt-10) cc_final: 0.5564 (tm-30) REVERT: A 738 GLU cc_start: 0.8205 (pt0) cc_final: 0.7986 (pt0) REVERT: A 763 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8027 (mtm) REVERT: A 781 MET cc_start: 0.7310 (ttp) cc_final: 0.6999 (ttt) REVERT: A 922 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7980 (mp0) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.0735 time to fit residues: 14.0430 Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 553 VAL Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 917 ILE 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: 0.7980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 105 optimal weight: 50.0000 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 GLN A 219 GLN A1038 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.200127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146296 restraints weight = 11564.848| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.54 r_work: 0.3343 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10147 Z= 0.120 Angle : 0.457 5.806 13985 Z= 0.253 Chirality : 0.036 0.158 1574 Planarity : 0.003 0.033 1530 Dihedral : 16.446 74.040 2245 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.20 % Allowed : 11.75 % Favored : 86.06 % 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: 2.19 (0.27), residues: 980 helix: 2.24 (0.21), residues: 579 sheet: 0.41 (0.87), residues: 41 loop : 0.36 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 94 TYR 0.015 0.001 TYR A 17 PHE 0.030 0.001 PHE A 513 TRP 0.010 0.001 TRP A1008 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (10147) covalent geometry : angle 0.45746 / 0.25 (13985) hydrogen bonds : bond 0.04998 / 3.29 ( 551) hydrogen bonds : angle 3.96264 / 2.86 ( 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 124 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.244 Fit side-chains REVERT: A 96 TYR cc_start: 0.8031 (t80) cc_final: 0.7825 (t80) REVERT: A 129 ASP cc_start: 0.8065 (m-30) cc_final: 0.7863 (m-30) REVERT: A 297 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: A 365 LEU cc_start: 0.6749 (tt) cc_final: 0.6295 (tp) REVERT: A 453 LYS cc_start: 0.8543 (mttt) cc_final: 0.8244 (mtmm) REVERT: A 520 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5459 (tm-30) REVERT: A 781 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6975 (ttt) REVERT: A 922 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8060 (mp0) REVERT: A 1013 TYR cc_start: 0.8552 (m-80) cc_final: 0.8100 (m-10) REVERT: A 1038 ASN cc_start: 0.8343 (m-40) cc_final: 0.7798 (t0) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.0677 time to fit residues: 11.9532 Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 976 SER 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: 5.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 549 HIS A 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.198086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144433 restraints weight = 11448.784| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.82 r_work: 0.3286 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10147 Z= 0.157 Angle : 0.487 6.575 13985 Z= 0.265 Chirality : 0.038 0.161 1574 Planarity : 0.004 0.035 1530 Dihedral : 16.437 74.180 2244 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.52 % Allowed : 12.07 % Favored : 85.40 % 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: 2.12 (0.27), residues: 980 helix: 2.21 (0.21), residues: 579 sheet: 0.21 (0.89), residues: 41 loop : 0.30 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.015 0.002 TYR A 17 PHE 0.019 0.002 PHE A 792 TRP 0.011 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10147) covalent geometry : angle 0.48704 / 0.26 (13985) hydrogen bonds : bond 0.04989 / 3.27 ( 551) hydrogen bonds : angle 3.93710 / 2.85 ( 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 125 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.252 Fit side-chains REVERT: A 94 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7665 (ttp80) REVERT: A 297 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: A 365 LEU cc_start: 0.6789 (tt) cc_final: 0.6342 (tp) REVERT: A 453 LYS cc_start: 0.8614 (mttt) cc_final: 0.8333 (mtmt) REVERT: A 520 GLU cc_start: 0.6403 (mt-10) cc_final: 0.5509 (tm-30) REVERT: A 738 GLU cc_start: 0.8232 (pt0) cc_final: 0.7982 (pt0) REVERT: A 781 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7065 (ttt) REVERT: A 1013 TYR cc_start: 0.8505 (m-80) cc_final: 0.7985 (m-10) REVERT: A 1038 ASN cc_start: 0.8260 (m-40) cc_final: 0.7739 (t0) REVERT: A 1077 MET cc_start: 0.8192 (mmt) cc_final: 0.7785 (mmt) outliers start: 23 outliers final: 15 residues processed: 121 average time/residue: 0.0782 time to fit residues: 13.5299 Evaluate side-chains 114 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 97 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.198962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143672 restraints weight = 11539.272| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.86 r_work: 0.3324 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10147 Z= 0.119 Angle : 0.446 5.840 13985 Z= 0.244 Chirality : 0.036 0.143 1574 Planarity : 0.004 0.043 1530 Dihedral : 16.405 73.993 2244 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 2.26 (0.27), residues: 980 helix: 2.31 (0.21), residues: 578 sheet: 0.44 (0.91), residues: 41 loop : 0.37 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.014 0.001 TYR A 17 PHE 0.018 0.001 PHE A 513 TRP 0.013 0.002 TRP A1008 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10147) covalent geometry : angle 0.44568 / 0.24 (13985) hydrogen bonds : bond 0.04609 / 3.03 ( 551) hydrogen bonds : angle 3.84313 / 2.78 ( 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 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.225 Fit side-chains REVERT: A 94 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7593 (ttp80) REVERT: A 105 ARG cc_start: 0.6511 (ptp90) cc_final: 0.6162 (ptt-90) REVERT: A 248 ARG cc_start: 0.8706 (mmt90) cc_final: 0.8469 (mmt-90) REVERT: A 297 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: A 365 LEU cc_start: 0.6650 (tt) cc_final: 0.6198 (tp) REVERT: A 393 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: A 453 LYS cc_start: 0.8625 (mttt) cc_final: 0.8267 (mtmm) REVERT: A 520 GLU cc_start: 0.6396 (mt-10) cc_final: 0.5478 (tm-30) REVERT: A 738 GLU cc_start: 0.8225 (pt0) cc_final: 0.7968 (pt0) REVERT: A 781 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7058 (ttt) REVERT: A 862 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7007 (mm-30) REVERT: A 930 MET cc_start: 0.7370 (ttp) cc_final: 0.7113 (ptp) REVERT: A 1013 TYR cc_start: 0.8480 (m-80) cc_final: 0.7927 (m-10) REVERT: A 1038 ASN cc_start: 0.8235 (m-40) cc_final: 0.7698 (t0) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 0.0816 time to fit residues: 14.4807 Evaluate side-chains 119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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 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 976 SER 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: 1.9990 chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.199742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145626 restraints weight = 11433.546| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.65 r_work: 0.3338 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10147 Z= 0.107 Angle : 0.436 6.938 13985 Z= 0.237 Chirality : 0.035 0.139 1574 Planarity : 0.003 0.033 1530 Dihedral : 16.320 73.946 2244 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.09 % Allowed : 12.73 % Favored : 85.18 % 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: 2.46 (0.27), residues: 980 helix: 2.45 (0.21), residues: 578 sheet: 0.59 (0.89), residues: 41 loop : 0.47 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 128 TYR 0.014 0.001 TYR A 17 PHE 0.016 0.001 PHE A 792 TRP 0.014 0.001 TRP A1008 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (10147) covalent geometry : angle 0.43588 / 0.24 (13985) hydrogen bonds : bond 0.04382 / 2.88 ( 551) hydrogen bonds : angle 3.78418 / 2.75 ( 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 125 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7582 (ttp80) REVERT: A 105 ARG cc_start: 0.6541 (ptp90) cc_final: 0.6009 (ptt-90) REVERT: A 248 ARG cc_start: 0.8680 (mmt90) cc_final: 0.8454 (mmt-90) REVERT: A 297 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: A 365 LEU cc_start: 0.6699 (tt) cc_final: 0.6273 (tp) REVERT: A 453 LYS cc_start: 0.8597 (mttt) cc_final: 0.8238 (mtmm) REVERT: A 520 GLU cc_start: 0.6400 (mt-10) cc_final: 0.5509 (tm-30) REVERT: A 738 GLU cc_start: 0.8195 (pt0) cc_final: 0.7943 (pt0) REVERT: A 781 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7074 (ttt) REVERT: A 831 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 862 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6891 (mm-30) REVERT: A 1013 TYR cc_start: 0.8449 (m-80) cc_final: 0.7925 (m-80) REVERT: A 1038 ASN cc_start: 0.8168 (m-40) cc_final: 0.7626 (t0) REVERT: A 1077 MET cc_start: 0.8145 (mmt) cc_final: 0.7884 (mmt) outliers start: 19 outliers final: 12 residues processed: 121 average time/residue: 0.0803 time to fit residues: 13.7176 Evaluate side-chains 119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 781 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 105 optimal weight: 50.0000 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.197889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143440 restraints weight = 11411.209| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.62 r_work: 0.3309 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10147 Z= 0.142 Angle : 0.469 9.567 13985 Z= 0.251 Chirality : 0.036 0.141 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.270 74.028 2241 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 2.42 (0.27), residues: 980 helix: 2.41 (0.21), residues: 578 sheet: 0.52 (0.84), residues: 43 loop : 0.50 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.016 0.002 TYR A 736 PHE 0.046 0.002 PHE A 513 TRP 0.015 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (10147) covalent geometry : angle 0.46933 / 0.25 (13985) hydrogen bonds : bond 0.04535 / 2.98 ( 551) hydrogen bonds : angle 3.83504 / 2.79 ( 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 127 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8636 (ttt) REVERT: A 94 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7565 (ttp80) REVERT: A 105 ARG cc_start: 0.6574 (ptp90) cc_final: 0.6011 (ptt-90) REVERT: A 248 ARG cc_start: 0.8707 (mmt90) cc_final: 0.8495 (mmt-90) REVERT: A 297 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: A 365 LEU cc_start: 0.6690 (tt) cc_final: 0.6235 (tp) REVERT: A 453 LYS cc_start: 0.8593 (mttt) cc_final: 0.8323 (mtmt) REVERT: A 520 GLU cc_start: 0.6430 (mt-10) cc_final: 0.5522 (tm-30) REVERT: A 729 MET cc_start: 0.7333 (tpp) cc_final: 0.7026 (tpp) REVERT: A 738 GLU cc_start: 0.8211 (pt0) cc_final: 0.7952 (pt0) REVERT: A 781 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7119 (ttt) REVERT: A 831 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6959 (mt-10) REVERT: A 862 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6877 (mm-30) REVERT: A 937 GLU cc_start: 0.7626 (tt0) cc_final: 0.7334 (tt0) REVERT: A 1013 TYR cc_start: 0.8421 (m-80) cc_final: 0.7885 (m-80) REVERT: A 1038 ASN cc_start: 0.8150 (m-40) cc_final: 0.7676 (t0) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 0.0837 time to fit residues: 14.4638 Evaluate side-chains 119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 781 MET 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: 2.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.197778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144138 restraints weight = 11488.519| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.54 r_work: 0.3316 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3569 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 : 0.465 8.022 13985 Z= 0.249 Chirality : 0.036 0.144 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.274 74.019 2241 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.31 % Allowed : 13.06 % Favored : 84.63 % 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: 2.43 (0.27), residues: 980 helix: 2.43 (0.21), residues: 577 sheet: 0.27 (0.81), residues: 43 loop : 0.52 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.014 0.001 TYR A 17 PHE 0.045 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 0.00320 / 0.14 (10147) covalent geometry : angle 0.46456 / 0.25 (13985) hydrogen bonds : bond 0.04479 / 2.93 ( 551) hydrogen bonds : angle 3.79777 / 2.77 ( 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 125 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.233 Fit side-chains REVERT: A 20 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8625 (ttt) REVERT: A 94 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7571 (ttp80) REVERT: A 105 ARG cc_start: 0.6623 (ptp90) cc_final: 0.6055 (ptt-90) REVERT: A 297 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: A 365 LEU cc_start: 0.6679 (tt) cc_final: 0.6253 (tp) REVERT: A 453 LYS cc_start: 0.8627 (mttt) cc_final: 0.8335 (mtmt) REVERT: A 520 GLU cc_start: 0.6470 (mt-10) cc_final: 0.5633 (tm-30) REVERT: A 564 MET cc_start: 0.6154 (mtp) cc_final: 0.5916 (mmm) REVERT: A 729 MET cc_start: 0.7369 (tpp) cc_final: 0.7074 (tpp) REVERT: A 738 GLU cc_start: 0.8185 (pt0) cc_final: 0.7932 (pt0) REVERT: A 781 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7148 (ttt) REVERT: A 831 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 937 GLU cc_start: 0.7645 (tt0) cc_final: 0.7379 (tt0) REVERT: A 1013 TYR cc_start: 0.8411 (m-80) cc_final: 0.8158 (m-10) REVERT: A 1038 ASN cc_start: 0.8143 (m-40) cc_final: 0.7728 (t0) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.0820 time to fit residues: 13.9438 Evaluate side-chains 119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.198524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145024 restraints weight = 11286.267| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.52 r_work: 0.3332 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10147 Z= 0.114 Angle : 0.460 9.858 13985 Z= 0.246 Chirality : 0.035 0.158 1574 Planarity : 0.004 0.049 1530 Dihedral : 16.253 73.906 2241 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.09 % Allowed : 13.06 % 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: 2.49 (0.27), residues: 980 helix: 2.49 (0.21), residues: 577 sheet: 0.27 (0.80), residues: 43 loop : 0.53 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 718 TYR 0.014 0.001 TYR A 17 PHE 0.040 0.001 PHE A 513 TRP 0.017 0.002 TRP A1008 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10147) covalent geometry : angle 0.45993 / 0.25 (13985) hydrogen bonds : bond 0.04323 / 2.84 ( 551) hydrogen bonds : angle 3.75914 / 2.74 ( 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 122 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.223 Fit side-chains REVERT: A 94 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7557 (ttp80) REVERT: A 105 ARG cc_start: 0.6604 (ptp90) cc_final: 0.6030 (ptt-90) REVERT: A 297 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: A 365 LEU cc_start: 0.6641 (tt) cc_final: 0.6211 (tp) REVERT: A 453 LYS cc_start: 0.8640 (mttt) cc_final: 0.8333 (mtmt) REVERT: A 520 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5610 (tm-30) REVERT: A 564 MET cc_start: 0.6164 (mtp) cc_final: 0.5868 (mmm) REVERT: A 729 MET cc_start: 0.7404 (tpp) cc_final: 0.7130 (tpp) REVERT: A 738 GLU cc_start: 0.8148 (pt0) cc_final: 0.7893 (pt0) REVERT: A 781 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7071 (ttt) REVERT: A 831 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6974 (mt-10) REVERT: A 1013 TYR cc_start: 0.8398 (m-80) cc_final: 0.8121 (m-10) REVERT: A 1038 ASN cc_start: 0.8126 (m-40) cc_final: 0.7708 (t0) REVERT: A 1077 MET cc_start: 0.8137 (mmt) cc_final: 0.7788 (mmt) outliers start: 19 outliers final: 13 residues processed: 119 average time/residue: 0.0840 time to fit residues: 14.1003 Evaluate side-chains 115 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 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 976 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 HIS A 722 ASN A 756 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.196362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142593 restraints weight = 11502.618| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.55 r_work: 0.3301 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10147 Z= 0.177 Angle : 0.509 9.447 13985 Z= 0.270 Chirality : 0.038 0.147 1574 Planarity : 0.004 0.038 1530 Dihedral : 16.264 74.160 2241 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.09 % Allowed : 13.06 % 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: 2.29 (0.27), residues: 980 helix: 2.31 (0.21), residues: 578 sheet: 0.14 (0.82), residues: 43 loop : 0.48 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 718 TYR 0.018 0.002 TYR A 736 PHE 0.055 0.002 PHE A 513 TRP 0.016 0.002 TRP A1008 HIS 0.004 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (10147) covalent geometry : angle 0.50863 / 0.27 (13985) hydrogen bonds : bond 0.04649 / 3.04 ( 551) hydrogen bonds : angle 3.87272 / 2.82 ( 1475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.88 seconds wall clock time: 34 minutes 23.92 seconds (2063.92 seconds total)