Starting phenix.real_space_refine on Fri Sep 11 08:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qfw_13950/09_2026/7qfw_13950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qfw_13950/09_2026/7qfw_13950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qfw_13950/09_2026/7qfw_13950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qfw_13950/09_2026/7qfw_13950.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qfw_13950/09_2026/7qfw_13950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qfw_13950/09_2026/7qfw_13950.map" } resolution = 3.86 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 32 5.16 5 C 5395 2.51 5 N 1492 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8765 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6643 Classifications: {'peptide': 823} Link IDs: {'PTRANS': 20, 'TRANS': 802} Chain breaks: 3 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 810 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 672 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 640 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 1.77, per 1000 atoms: 0.20 Number of scatterers: 8765 At special positions: 0 Unit cell: (79.04, 111.28, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 64 15.00 O 1782 8.00 N 1492 7.00 C 5395 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: 0.94 Conformation dependent library (CDL) restraints added in 252.7 milliseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 73.9% alpha, 0.0% beta 30 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 8 through 24 removed outlier: 4.032A pdb=" N PHE A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 49 removed outlier: 3.811A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 72 through 98 removed outlier: 3.737A pdb=" N ASP A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.629A pdb=" N ARG A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.780A pdb=" N ARG A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.112A pdb=" N GLY A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.658A pdb=" N ARG A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.949A pdb=" N THR A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.540A pdb=" N ALA A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.571A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.699A pdb=" N PHE A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 272 through 285 removed outlier: 3.734A pdb=" N GLN A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.508A pdb=" N ARG A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.791A pdb=" N ILE A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 351' Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 384 through 401 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 474 through 500 removed outlier: 3.681A pdb=" N PHE A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 3.502A pdb=" N ILE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.655A pdb=" N ARG A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 631 Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.837A pdb=" N ALA A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR A 642 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 671 Processing helix chain 'A' and resid 682 through 695 Processing helix chain 'A' and resid 699 through 716 Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 740 through 751 removed outlier: 3.659A pdb=" N ILE A 751 " --> pdb=" O PHE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 758 removed outlier: 3.760A pdb=" N SER A 757 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 785 removed outlier: 4.404A pdb=" N ALA A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.711A pdb=" N LYS A 823 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 825 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 839 Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.886A pdb=" N ALA A 857 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 858 " --> pdb=" O ILE A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'A' and resid 866 through 883 removed outlier: 4.207A pdb=" N LEU A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 883 " --> pdb=" O ILE A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 908 removed outlier: 4.311A pdb=" N ALA A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 486 through 490 removed outlier: 3.519A pdb=" N ASN B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 511 421 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2296 1.34 - 1.45: 1885 1.45 - 1.57: 4689 1.57 - 1.69: 126 1.69 - 1.81: 50 Bond restraints: 9046 Sorted by residual: bond pdb=" C3' DT D 15 " pdb=" C2' DT D 15 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" CA ASN A 672 " pdb=" C ASN A 672 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.40e-02 5.10e+03 9.69e+00 bond pdb=" C4' DA C 17 " pdb=" C3' DA C 17 " ideal model delta sigma weight residual 1.529 1.501 0.028 1.00e-02 1.00e+04 8.11e+00 bond pdb=" N9 DA C 12 " pdb=" C4 DA C 12 " ideal model delta sigma weight residual 1.374 1.358 0.016 6.00e-03 2.78e+04 7.43e+00 bond pdb=" C1' DA C 12 " pdb=" N9 DA C 12 " ideal model delta sigma weight residual 1.468 1.435 0.033 1.40e-02 5.10e+03 5.41e+00 ... (remaining 9041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 12290 3.09 - 6.19: 188 6.19 - 9.28: 12 9.28 - 12.37: 3 12.37 - 15.47: 1 Bond angle restraints: 12494 Sorted by residual: angle pdb=" C3' DT D 9 " pdb=" O3' DT D 9 " pdb=" P DT D 10 " ideal model delta sigma weight residual 119.70 127.45 -7.75 1.20e+00 6.94e-01 4.17e+01 angle pdb=" C3' DT D 10 " pdb=" C2' DT D 10 " pdb=" C1' DT D 10 " ideal model delta sigma weight residual 102.50 96.10 6.40 1.20e+00 6.94e-01 2.84e+01 angle pdb=" O4' DA C 17 " pdb=" C4' DA C 17 " pdb=" C3' DA C 17 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.87 -2.97 6.00e-01 2.78e+00 2.46e+01 angle pdb=" C LYS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 ... (remaining 12489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.37: 4651 27.37 - 54.74: 670 54.74 - 82.11: 81 82.11 - 109.48: 6 109.48 - 136.84: 2 Dihedral angle restraints: 5410 sinusoidal: 2689 harmonic: 2721 Sorted by residual: dihedral pdb=" CA LYS A 98 " pdb=" C LYS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP B 462 " pdb=" C ASP B 462 " pdb=" N PHE B 463 " pdb=" CA PHE B 463 " ideal model delta harmonic sigma weight residual 180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN A 818 " pdb=" C GLN A 818 " pdb=" N THR A 819 " pdb=" CA THR A 819 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1003 0.049 - 0.097: 337 0.097 - 0.146: 76 0.146 - 0.194: 18 0.194 - 0.243: 4 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C3' DT D 15 " pdb=" C4' DT D 15 " pdb=" O3' DT D 15 " pdb=" C2' DT D 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" P DT D 10 " pdb=" OP1 DT D 10 " pdb=" OP2 DT D 10 " pdb=" O5' DT D 10 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1' DA C 16 " pdb=" O4' DA C 16 " pdb=" C2' DA C 16 " pdb=" N9 DA C 16 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1435 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 66 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 67 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 608 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO A 609 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 609 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 609 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 798 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO A 799 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 799 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 799 " 0.038 5.00e-02 4.00e+02 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2303 2.80 - 3.33: 8063 3.33 - 3.85: 15330 3.85 - 4.38: 17579 4.38 - 4.90: 27470 Nonbonded interactions: 70745 Sorted by model distance: nonbonded pdb=" O PRO A 383 " pdb=" OH TYR A 432 " model vdw 2.276 3.040 nonbonded pdb=" O THR A 826 " pdb=" OG1 THR A 830 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 862 " pdb=" OG SER A 862 " model vdw 2.329 3.040 nonbonded pdb=" O GLU A 430 " pdb=" OG SER A 470 " model vdw 2.337 3.040 nonbonded pdb=" O THR A 727 " pdb=" OG SER A 731 " model vdw 2.346 3.040 ... (remaining 70740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.480 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9046 Z= 0.368 Angle : 1.032 15.467 12494 Z= 0.723 Chirality : 0.052 0.243 1438 Planarity : 0.008 0.079 1373 Dihedral : 22.546 136.844 3624 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.36 % Allowed : 6.92 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.20), residues: 905 helix: -2.90 (0.14), residues: 630 sheet: None (None), residues: 0 loop : -3.13 (0.29), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 322 TYR 0.018 0.002 TYR B 496 PHE 0.023 0.002 PHE A 354 TRP 0.014 0.002 TRP A 780 HIS 0.008 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.37 ( 9046) covalent geometry : angle 1.03226 / 0.72 (12494) hydrogen bonds : bond 0.12665 / 8.31 ( 481) hydrogen bonds : angle 6.10970 / 4.31 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7665 (mttm) cc_final: 0.7383 (mmtp) REVERT: A 13 ILE cc_start: 0.7989 (mm) cc_final: 0.7588 (mt) REVERT: A 39 LYS cc_start: 0.7811 (tptt) cc_final: 0.7555 (tptt) REVERT: A 47 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6286 (tm-30) REVERT: A 72 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 107 GLU cc_start: 0.8005 (mp0) cc_final: 0.7696 (mm-30) REVERT: A 136 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6952 (mmt-90) REVERT: A 266 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7733 (mtmm) REVERT: A 285 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6819 (mm-30) REVERT: A 384 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6239 (tm-30) REVERT: A 421 ILE cc_start: 0.6590 (mt) cc_final: 0.6382 (mm) REVERT: A 471 LEU cc_start: 0.7946 (tp) cc_final: 0.7728 (tp) REVERT: A 641 MET cc_start: 0.7488 (tpp) cc_final: 0.7090 (tpt) REVERT: A 644 LEU cc_start: 0.8161 (mt) cc_final: 0.7892 (mp) REVERT: A 648 VAL cc_start: 0.7331 (p) cc_final: 0.7100 (p) REVERT: A 695 LYS cc_start: 0.7067 (mttt) cc_final: 0.6844 (mttp) REVERT: A 705 ILE cc_start: 0.8051 (pt) cc_final: 0.7700 (mt) REVERT: A 808 PHE cc_start: 0.7944 (t80) cc_final: 0.7720 (t80) REVERT: A 837 LYS cc_start: 0.7459 (mttm) cc_final: 0.7234 (ttmm) REVERT: A 841 GLN cc_start: 0.7527 (mt0) cc_final: 0.7210 (tt0) REVERT: A 895 LYS cc_start: 0.7385 (tttt) cc_final: 0.7183 (ttpt) REVERT: B 408 TRP cc_start: 0.6047 (p-90) cc_final: 0.4805 (p-90) outliers start: 3 outliers final: 0 residues processed: 195 average time/residue: 0.1130 time to fit residues: 29.2445 Evaluate side-chains 174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 31 HIS A 42 GLN A 71 ASN A 121 HIS A 216 ASN A 372 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 402 HIS A 613 ASN A 661 GLN A 697 ASN A 884 ASN B 401 ASN B 495 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.162993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140119 restraints weight = 12723.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.143796 restraints weight = 6882.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.146258 restraints weight = 4307.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147746 restraints weight = 3043.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149050 restraints weight = 2381.649| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9046 Z= 0.192 Angle : 0.723 10.844 12494 Z= 0.399 Chirality : 0.047 0.303 1438 Planarity : 0.006 0.061 1373 Dihedral : 25.152 146.355 1749 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.43 % Allowed : 14.32 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.24), residues: 905 helix: -1.43 (0.18), residues: 632 sheet: None (None), residues: 0 loop : -2.97 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 910 TYR 0.016 0.002 TYR A 657 PHE 0.018 0.002 PHE A 362 TRP 0.008 0.001 TRP B 408 HIS 0.008 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 9046) covalent geometry : angle 0.72318 / 0.40 (12494) hydrogen bonds : bond 0.06053 / 3.82 ( 481) hydrogen bonds : angle 4.65396 / 3.23 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7677 (mttm) cc_final: 0.7335 (mmtp) REVERT: A 13 ILE cc_start: 0.8005 (mm) cc_final: 0.7616 (mt) REVERT: A 39 LYS cc_start: 0.7858 (tptt) cc_final: 0.7620 (tptt) REVERT: A 72 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 107 GLU cc_start: 0.7951 (mp0) cc_final: 0.7688 (mm-30) REVERT: A 190 GLN cc_start: 0.7816 (mp10) cc_final: 0.7604 (mp10) REVERT: A 227 MET cc_start: 0.7148 (ttm) cc_final: 0.6900 (ttm) REVERT: A 284 LEU cc_start: 0.8391 (mt) cc_final: 0.8170 (mt) REVERT: A 288 GLU cc_start: 0.6672 (tm-30) cc_final: 0.6304 (tm-30) REVERT: A 291 VAL cc_start: 0.7363 (p) cc_final: 0.7145 (m) REVERT: A 333 LEU cc_start: 0.8104 (mt) cc_final: 0.7711 (tp) REVERT: A 450 MET cc_start: 0.6252 (ttp) cc_final: 0.6024 (ttp) REVERT: A 489 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7459 (tt) REVERT: A 692 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7524 (mmmt) REVERT: A 695 LYS cc_start: 0.7118 (mttt) cc_final: 0.6863 (mttp) REVERT: A 705 ILE cc_start: 0.7841 (pt) cc_final: 0.7564 (mt) REVERT: A 767 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7505 (mtm-85) REVERT: A 816 VAL cc_start: 0.8557 (p) cc_final: 0.8315 (t) REVERT: A 824 LYS cc_start: 0.7548 (mttm) cc_final: 0.7261 (mmtp) REVERT: A 837 LYS cc_start: 0.7473 (mttm) cc_final: 0.7229 (ttmm) REVERT: A 841 GLN cc_start: 0.7594 (mt0) cc_final: 0.7291 (tt0) REVERT: A 895 LYS cc_start: 0.7395 (tttt) cc_final: 0.7136 (ttpt) REVERT: B 492 ASN cc_start: 0.8211 (t0) cc_final: 0.7822 (m-40) outliers start: 12 outliers final: 4 residues processed: 190 average time/residue: 0.1057 time to fit residues: 26.8370 Evaluate side-chains 181 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS A 121 HIS ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 HIS B 495 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.140660 restraints weight = 12614.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.144299 restraints weight = 6832.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.146855 restraints weight = 4297.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.148511 restraints weight = 3017.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149757 restraints weight = 2320.347| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9046 Z= 0.166 Angle : 0.670 10.351 12494 Z= 0.371 Chirality : 0.045 0.308 1438 Planarity : 0.005 0.055 1373 Dihedral : 25.017 145.237 1749 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 16.47 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.25), residues: 905 helix: -0.77 (0.19), residues: 618 sheet: None (None), residues: 0 loop : -2.75 (0.30), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 581 TYR 0.014 0.001 TYR A 657 PHE 0.012 0.001 PHE B 504 TRP 0.012 0.001 TRP B 408 HIS 0.006 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 9046) covalent geometry : angle 0.67019 / 0.37 (12494) hydrogen bonds : bond 0.05571 / 3.53 ( 481) hydrogen bonds : angle 4.35384 / 3.00 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7561 (mttm) cc_final: 0.7324 (mmtp) REVERT: A 13 ILE cc_start: 0.7996 (mm) cc_final: 0.7618 (mt) REVERT: A 19 GLU cc_start: 0.7151 (tt0) cc_final: 0.6901 (tt0) REVERT: A 39 LYS cc_start: 0.7819 (tptt) cc_final: 0.7530 (tptt) REVERT: A 65 ILE cc_start: 0.7182 (tt) cc_final: 0.6978 (tt) REVERT: A 72 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7443 (tm-30) REVERT: A 107 GLU cc_start: 0.7970 (mp0) cc_final: 0.7690 (mm-30) REVERT: A 118 PHE cc_start: 0.7564 (t80) cc_final: 0.7364 (t80) REVERT: A 333 LEU cc_start: 0.8072 (mt) cc_final: 0.7716 (tp) REVERT: A 353 ASP cc_start: 0.6634 (t0) cc_final: 0.6350 (t0) REVERT: A 391 HIS cc_start: 0.6527 (m-70) cc_final: 0.6286 (m170) REVERT: A 450 MET cc_start: 0.6270 (ttp) cc_final: 0.6008 (ttp) REVERT: A 692 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7582 (mmmt) REVERT: A 705 ILE cc_start: 0.7848 (pt) cc_final: 0.7525 (tp) REVERT: A 753 VAL cc_start: 0.8130 (p) cc_final: 0.7856 (t) REVERT: A 841 GLN cc_start: 0.7586 (mt0) cc_final: 0.7331 (tt0) REVERT: A 895 LYS cc_start: 0.7415 (tttt) cc_final: 0.7155 (ttpt) REVERT: B 492 ASN cc_start: 0.8209 (t0) cc_final: 0.7762 (m-40) outliers start: 17 outliers final: 9 residues processed: 184 average time/residue: 0.0983 time to fit residues: 24.3517 Evaluate side-chains 173 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 424 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138668 restraints weight = 12745.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142543 restraints weight = 6876.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145133 restraints weight = 4304.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.146716 restraints weight = 3023.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.148033 restraints weight = 2365.766| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9046 Z= 0.172 Angle : 0.672 10.438 12494 Z= 0.368 Chirality : 0.045 0.310 1438 Planarity : 0.005 0.061 1373 Dihedral : 24.949 146.523 1749 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.39 % Allowed : 18.14 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.25), residues: 905 helix: -0.57 (0.19), residues: 630 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 581 TYR 0.015 0.002 TYR A 657 PHE 0.013 0.001 PHE B 523 TRP 0.007 0.001 TRP A 780 HIS 0.007 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 9046) covalent geometry : angle 0.67181 / 0.37 (12494) hydrogen bonds : bond 0.05488 / 3.47 ( 481) hydrogen bonds : angle 4.23698 / 2.92 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.7121 (tt0) cc_final: 0.6853 (tt0) REVERT: A 39 LYS cc_start: 0.7846 (tptt) cc_final: 0.7564 (tptt) REVERT: A 72 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 107 GLU cc_start: 0.7966 (mp0) cc_final: 0.7749 (mm-30) REVERT: A 118 PHE cc_start: 0.7604 (t80) cc_final: 0.7392 (t80) REVERT: A 221 GLU cc_start: 0.6720 (tp30) cc_final: 0.6464 (tp30) REVERT: A 333 LEU cc_start: 0.8043 (mt) cc_final: 0.7686 (tp) REVERT: A 353 ASP cc_start: 0.6632 (t0) cc_final: 0.6295 (t0) REVERT: A 692 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7592 (mmmt) REVERT: A 705 ILE cc_start: 0.7884 (pt) cc_final: 0.7598 (tp) REVERT: A 895 LYS cc_start: 0.7471 (tttt) cc_final: 0.7223 (ttpt) REVERT: B 492 ASN cc_start: 0.8184 (t0) cc_final: 0.7770 (m-40) outliers start: 20 outliers final: 10 residues processed: 175 average time/residue: 0.1025 time to fit residues: 24.5184 Evaluate side-chains 170 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.0010 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.163519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139639 restraints weight = 12618.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143432 restraints weight = 6870.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145949 restraints weight = 4328.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.147551 restraints weight = 3066.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148831 restraints weight = 2398.342| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9046 Z= 0.158 Angle : 0.661 10.420 12494 Z= 0.363 Chirality : 0.044 0.314 1438 Planarity : 0.005 0.050 1373 Dihedral : 24.905 147.137 1749 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.51 % Allowed : 18.38 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.26), residues: 905 helix: -0.39 (0.20), residues: 633 sheet: None (None), residues: 0 loop : -2.73 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 910 TYR 0.014 0.001 TYR A 657 PHE 0.010 0.001 PHE B 504 TRP 0.008 0.001 TRP A 780 HIS 0.022 0.002 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 9046) covalent geometry : angle 0.66141 / 0.36 (12494) hydrogen bonds : bond 0.05355 / 3.39 ( 481) hydrogen bonds : angle 4.19634 / 2.88 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8048 (mm) cc_final: 0.7734 (mt) REVERT: A 19 GLU cc_start: 0.7106 (tt0) cc_final: 0.6841 (tt0) REVERT: A 39 LYS cc_start: 0.7856 (tptt) cc_final: 0.7573 (tptt) REVERT: A 72 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 107 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: A 333 LEU cc_start: 0.8050 (mt) cc_final: 0.7690 (tp) REVERT: A 353 ASP cc_start: 0.6632 (t0) cc_final: 0.6321 (t0) REVERT: A 384 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6662 (tm-30) REVERT: A 450 MET cc_start: 0.6296 (ttp) cc_final: 0.6095 (ttp) REVERT: A 692 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7600 (mmmt) REVERT: A 895 LYS cc_start: 0.7497 (tttt) cc_final: 0.7237 (ttpt) REVERT: B 492 ASN cc_start: 0.8152 (t0) cc_final: 0.7740 (m-40) outliers start: 21 outliers final: 12 residues processed: 169 average time/residue: 0.0996 time to fit residues: 23.0642 Evaluate side-chains 172 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.2980 chunk 76 optimal weight: 0.4980 chunk 93 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN A 670 HIS B 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139686 restraints weight = 12764.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143492 restraints weight = 6917.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.145948 restraints weight = 4348.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.147766 restraints weight = 3071.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148792 restraints weight = 2370.553| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9046 Z= 0.156 Angle : 0.655 10.361 12494 Z= 0.359 Chirality : 0.044 0.316 1438 Planarity : 0.005 0.061 1373 Dihedral : 24.849 148.419 1749 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.63 % Allowed : 19.33 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.26), residues: 905 helix: -0.23 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.68 (0.31), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 910 TYR 0.014 0.001 TYR A 657 PHE 0.025 0.001 PHE A 118 TRP 0.008 0.001 TRP A 780 HIS 0.006 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 9046) covalent geometry : angle 0.65493 / 0.36 (12494) hydrogen bonds : bond 0.05289 / 3.35 ( 481) hydrogen bonds : angle 4.10263 / 2.82 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8093 (mm) cc_final: 0.7773 (mt) REVERT: A 19 GLU cc_start: 0.7081 (tt0) cc_final: 0.6820 (tt0) REVERT: A 31 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.6443 (m-70) REVERT: A 39 LYS cc_start: 0.7836 (tptt) cc_final: 0.7581 (tptt) REVERT: A 72 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 107 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: A 252 ARG cc_start: 0.7318 (mtm110) cc_final: 0.6790 (mtm180) REVERT: A 333 LEU cc_start: 0.8044 (mt) cc_final: 0.7683 (tp) REVERT: A 353 ASP cc_start: 0.6550 (t0) cc_final: 0.6190 (t0) REVERT: A 384 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6595 (tm-30) REVERT: A 692 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7642 (mmmt) REVERT: A 852 ILE cc_start: 0.7876 (mm) cc_final: 0.7663 (mm) REVERT: B 492 ASN cc_start: 0.8118 (t0) cc_final: 0.7661 (m-40) outliers start: 22 outliers final: 15 residues processed: 171 average time/residue: 0.1021 time to fit residues: 23.5460 Evaluate side-chains 176 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 88 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 0.0050 chunk 28 optimal weight: 0.8980 overall best weight: 0.1870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS A 401 HIS A 424 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.162994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140767 restraints weight = 12803.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.144107 restraints weight = 7229.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146388 restraints weight = 4673.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147940 restraints weight = 3363.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149019 restraints weight = 2645.849| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9046 Z= 0.128 Angle : 0.637 10.151 12494 Z= 0.349 Chirality : 0.043 0.325 1438 Planarity : 0.004 0.045 1373 Dihedral : 24.738 148.936 1749 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.74 % Allowed : 19.69 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 905 helix: -0.00 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -2.70 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 910 TYR 0.011 0.001 TYR A 584 PHE 0.020 0.001 PHE A 118 TRP 0.011 0.001 TRP A 780 HIS 0.005 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9046) covalent geometry : angle 0.63667 / 0.35 (12494) hydrogen bonds : bond 0.04959 / 3.13 ( 481) hydrogen bonds : angle 3.93919 / 2.70 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8049 (mm) cc_final: 0.7729 (mt) REVERT: A 39 LYS cc_start: 0.7773 (tptt) cc_final: 0.7534 (tptt) REVERT: A 252 ARG cc_start: 0.7359 (mtm110) cc_final: 0.6720 (mtm180) REVERT: A 291 VAL cc_start: 0.7464 (m) cc_final: 0.6877 (p) REVERT: A 333 LEU cc_start: 0.7985 (mt) cc_final: 0.7687 (tt) REVERT: A 353 ASP cc_start: 0.6473 (t0) cc_final: 0.6130 (t0) REVERT: A 384 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6682 (tm-30) REVERT: A 443 MET cc_start: 0.7729 (tpp) cc_final: 0.7388 (tpt) REVERT: A 692 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7649 (mmmt) REVERT: A 852 ILE cc_start: 0.7948 (mm) cc_final: 0.7702 (mm) REVERT: B 408 TRP cc_start: 0.5525 (p-90) cc_final: 0.5109 (p-90) REVERT: B 492 ASN cc_start: 0.7878 (t0) cc_final: 0.7449 (m-40) outliers start: 23 outliers final: 14 residues processed: 172 average time/residue: 0.1029 time to fit residues: 23.8906 Evaluate side-chains 173 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141106 restraints weight = 12689.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144841 restraints weight = 6949.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147474 restraints weight = 4399.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149234 restraints weight = 3095.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150451 restraints weight = 2386.270| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9046 Z= 0.147 Angle : 0.643 9.862 12494 Z= 0.352 Chirality : 0.043 0.319 1438 Planarity : 0.005 0.064 1373 Dihedral : 24.709 150.816 1749 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.15 % Allowed : 21.24 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.27), residues: 905 helix: -0.00 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -2.80 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 581 TYR 0.012 0.001 TYR A 395 PHE 0.014 0.001 PHE A 118 TRP 0.007 0.001 TRP A 780 HIS 0.011 0.002 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 9046) covalent geometry : angle 0.64295 / 0.35 (12494) hydrogen bonds : bond 0.04999 / 3.17 ( 481) hydrogen bonds : angle 3.97177 / 2.73 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8069 (mm) cc_final: 0.7750 (mt) REVERT: A 19 GLU cc_start: 0.7102 (tt0) cc_final: 0.6854 (tt0) REVERT: A 39 LYS cc_start: 0.7799 (tptt) cc_final: 0.7582 (tptt) REVERT: A 333 LEU cc_start: 0.8042 (mt) cc_final: 0.7725 (tp) REVERT: A 384 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6519 (tm-30) REVERT: A 443 MET cc_start: 0.7618 (tpp) cc_final: 0.7286 (tpt) REVERT: A 581 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7487 (mtt-85) REVERT: A 692 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7696 (mmmt) REVERT: A 852 ILE cc_start: 0.8032 (mm) cc_final: 0.7792 (mm) REVERT: B 492 ASN cc_start: 0.7858 (t0) cc_final: 0.7474 (m-40) outliers start: 18 outliers final: 16 residues processed: 168 average time/residue: 0.1069 time to fit residues: 24.2459 Evaluate side-chains 173 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 5 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140070 restraints weight = 12625.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.143784 restraints weight = 6903.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146392 restraints weight = 4370.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147966 restraints weight = 3089.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149266 restraints weight = 2414.126| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9046 Z= 0.166 Angle : 0.667 9.554 12494 Z= 0.363 Chirality : 0.045 0.318 1438 Planarity : 0.005 0.056 1373 Dihedral : 24.661 151.830 1749 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.39 % Allowed : 21.12 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.27), residues: 905 helix: -0.04 (0.20), residues: 643 sheet: None (None), residues: 0 loop : -2.67 (0.31), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 910 TYR 0.013 0.001 TYR A 395 PHE 0.014 0.001 PHE A 118 TRP 0.007 0.001 TRP B 408 HIS 0.011 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 9046) covalent geometry : angle 0.66662 / 0.36 (12494) hydrogen bonds : bond 0.05042 / 3.21 ( 481) hydrogen bonds : angle 4.02098 / 2.77 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8085 (mm) cc_final: 0.7769 (mt) REVERT: A 19 GLU cc_start: 0.7069 (tt0) cc_final: 0.6821 (tt0) REVERT: A 39 LYS cc_start: 0.7864 (tptt) cc_final: 0.7648 (tptt) REVERT: A 333 LEU cc_start: 0.8067 (mt) cc_final: 0.7727 (tp) REVERT: A 384 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6709 (tm-30) REVERT: A 443 MET cc_start: 0.7706 (tpp) cc_final: 0.7336 (tpt) REVERT: A 581 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7470 (mtt-85) REVERT: A 692 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7705 (mmmt) REVERT: A 852 ILE cc_start: 0.8056 (mm) cc_final: 0.7824 (mm) REVERT: B 492 ASN cc_start: 0.7879 (t0) cc_final: 0.7518 (m-40) outliers start: 20 outliers final: 16 residues processed: 167 average time/residue: 0.1079 time to fit residues: 24.3195 Evaluate side-chains 174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.164115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140535 restraints weight = 12645.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144281 restraints weight = 6887.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.146857 restraints weight = 4339.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148613 restraints weight = 3056.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149764 restraints weight = 2360.391| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9046 Z= 0.155 Angle : 0.657 9.242 12494 Z= 0.358 Chirality : 0.044 0.319 1438 Planarity : 0.005 0.057 1373 Dihedral : 24.615 152.329 1749 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.39 % Allowed : 20.76 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.27), residues: 905 helix: 0.06 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.65 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 910 TYR 0.013 0.001 TYR A 395 PHE 0.014 0.001 PHE A 118 TRP 0.016 0.001 TRP B 408 HIS 0.010 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 9046) covalent geometry : angle 0.65717 / 0.36 (12494) hydrogen bonds : bond 0.05017 / 3.20 ( 481) hydrogen bonds : angle 3.99290 / 2.75 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8089 (mm) cc_final: 0.7775 (mt) REVERT: A 19 GLU cc_start: 0.7106 (tt0) cc_final: 0.6880 (tt0) REVERT: A 39 LYS cc_start: 0.7856 (tptt) cc_final: 0.7651 (tptt) REVERT: A 288 GLU cc_start: 0.6106 (tm-30) cc_final: 0.5786 (tt0) REVERT: A 291 VAL cc_start: 0.7238 (m) cc_final: 0.6980 (p) REVERT: A 333 LEU cc_start: 0.8045 (mt) cc_final: 0.7713 (tp) REVERT: A 384 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 443 MET cc_start: 0.7682 (tpp) cc_final: 0.7299 (tpt) REVERT: A 581 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7448 (mtt-85) REVERT: A 692 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7697 (mmmt) REVERT: A 852 ILE cc_start: 0.8044 (mm) cc_final: 0.7807 (mm) outliers start: 20 outliers final: 18 residues processed: 170 average time/residue: 0.1072 time to fit residues: 24.6877 Evaluate side-chains 175 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.165018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.141327 restraints weight = 12569.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145180 restraints weight = 6839.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147769 restraints weight = 4281.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.149382 restraints weight = 3013.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150690 restraints weight = 2337.880| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9046 Z= 0.135 Angle : 0.643 9.110 12494 Z= 0.350 Chirality : 0.044 0.314 1438 Planarity : 0.005 0.058 1373 Dihedral : 24.537 152.817 1749 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.51 % Allowed : 20.76 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.27), residues: 905 helix: 0.21 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -2.66 (0.30), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 910 TYR 0.013 0.001 TYR A 395 PHE 0.015 0.001 PHE A 118 TRP 0.009 0.001 TRP A 780 HIS 0.009 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9046) covalent geometry : angle 0.64266 / 0.35 (12494) hydrogen bonds : bond 0.04836 / 3.08 ( 481) hydrogen bonds : angle 3.91903 / 2.70 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.19 seconds wall clock time: 26 minutes 46.74 seconds (1606.74 seconds total)