Starting phenix.real_space_refine on Tue Mar 3 15:18:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ix6_60965/03_2026/9ix6_60965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ix6_60965/03_2026/9ix6_60965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ix6_60965/03_2026/9ix6_60965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ix6_60965/03_2026/9ix6_60965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ix6_60965/03_2026/9ix6_60965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ix6_60965/03_2026/9ix6_60965.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 38 5.49 5 S 17 5.16 5 C 3875 2.51 5 N 1105 2.21 5 O 1281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6316 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "A" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5398 Classifications: {'peptide': 651} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 638} Chain breaks: 8 Chain: "B" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 809 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 15, 'rna3p_pyr': 14} Link IDs: {'rna2p': 9, 'rna3p': 28} Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6316 At special positions: 0 Unit cell: (67.98, 99.66, 100.98, 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 17 16.00 P 38 15.00 O 1281 8.00 N 1105 7.00 C 3875 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: 0.63 Conformation dependent library (CDL) restraints added in 206.9 milliseconds 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 48.0% alpha, 14.3% beta 5 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.720A pdb=" N TYR A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 removed outlier: 4.262A pdb=" N GLU A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 5.282A pdb=" N ARG A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 272 " --> pdb=" O TRP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.894A pdb=" N PHE A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 4.304A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.138A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 461 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 537 through 565 removed outlier: 3.713A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A 542 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.716A pdb=" N PHE A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 610 " --> pdb=" O ASP A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 610' Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.740A pdb=" N ALA A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 657 Processing helix chain 'A' and resid 657 through 667 removed outlier: 3.813A pdb=" N VAL A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 700 Processing helix chain 'A' and resid 715 through 744 removed outlier: 4.293A pdb=" N TYR A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 767 removed outlier: 3.992A pdb=" N LYS A 767 " --> pdb=" O SER A 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 764 through 767' Processing helix chain 'A' and resid 768 through 774 removed outlier: 4.211A pdb=" N ILE A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 3.968A pdb=" N VAL A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 781 " --> pdb=" O ARG A 777 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.692A pdb=" N LEU A 805 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 3.733A pdb=" N GLY A 829 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 848 removed outlier: 3.707A pdb=" N THR A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 844 " --> pdb=" O SER A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 890 removed outlier: 3.764A pdb=" N SER A 884 " --> pdb=" O THR A 880 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 888 " --> pdb=" O SER A 884 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR A 889 " --> pdb=" O TYR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 Processing helix chain 'A' and resid 933 through 951 removed outlier: 3.622A pdb=" N ILE A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 6 through 11 removed outlier: 3.539A pdb=" N VAL A 442 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A 427 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.813A pdb=" N GLY A 347 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 349 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.844A pdb=" N TYR A 406 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 423 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 408 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 410 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 509 through 512 removed outlier: 3.924A pdb=" N GLY A 522 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE A 497 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 529 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET A 495 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 752 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 570 through 572 removed outlier: 4.148A pdb=" N THR A 571 " --> pdb=" O CYS A 582 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 904 removed outlier: 3.632A pdb=" N ILE A 896 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ALA A 895 " --> pdb=" O VAL A 874 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 872 " --> pdb=" O LEU A 897 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 871 " --> pdb=" O LYS A 863 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 863 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N MET A 858 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU A 923 " --> pdb=" O MET A 858 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 860 " --> pdb=" O VAL A 921 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL A 921 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 862 " --> pdb=" O SER A 919 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS A 917 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 930 " --> pdb=" O HIS A 927 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.81 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: 1800 1.34 - 1.45: 1275 1.45 - 1.57: 3346 1.57 - 1.69: 75 1.69 - 1.81: 25 Bond restraints: 6521 Sorted by residual: bond pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.96e+00 bond pdb=" N LEU A 218 " pdb=" CA LEU A 218 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.41e+00 bond pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta sigma weight residual 1.461 1.485 -0.024 1.17e-02 7.31e+03 4.07e+00 bond pdb=" N GLU A 448 " pdb=" CA GLU A 448 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.29e-02 6.01e+03 3.87e+00 bond pdb=" N LYS C 3 " pdb=" CA LYS C 3 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 ... (remaining 6516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8703 1.69 - 3.39: 217 3.39 - 5.08: 31 5.08 - 6.78: 9 6.78 - 8.47: 2 Bond angle restraints: 8962 Sorted by residual: angle pdb=" C ILE A 221 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " ideal model delta sigma weight residual 120.29 114.34 5.95 1.42e+00 4.96e-01 1.76e+01 angle pdb=" CB LYS A 917 " pdb=" CG LYS A 917 " pdb=" CD LYS A 917 " ideal model delta sigma weight residual 111.30 119.77 -8.47 2.30e+00 1.89e-01 1.36e+01 angle pdb=" CA ILE A 221 " pdb=" C ILE A 221 " pdb=" O ILE A 221 " ideal model delta sigma weight residual 121.05 117.51 3.54 1.04e+00 9.25e-01 1.16e+01 angle pdb=" N GLU A 220 " pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " ideal model delta sigma weight residual 109.91 114.81 -4.90 1.46e+00 4.69e-01 1.13e+01 angle pdb=" CA VAL A 381 " pdb=" CB VAL A 381 " pdb=" CG1 VAL A 381 " ideal model delta sigma weight residual 110.40 115.78 -5.38 1.70e+00 3.46e-01 1.00e+01 ... (remaining 8957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 3681 34.55 - 69.10: 257 69.10 - 103.65: 23 103.65 - 138.19: 0 138.19 - 172.74: 2 Dihedral angle restraints: 3963 sinusoidal: 2001 harmonic: 1962 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 44.74 -172.74 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual 70.00 1.20 68.80 1 2.00e+01 2.50e-03 1.53e+01 dihedral pdb=" C4' U B -6 " pdb=" C3' U B -6 " pdb=" O3' U B -6 " pdb=" P U B -5 " ideal model delta sinusoidal sigma weight residual -140.00 19.10 -159.10 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 3960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 710 0.037 - 0.074: 194 0.074 - 0.111: 83 0.111 - 0.147: 14 0.147 - 0.184: 6 Chirality restraints: 1007 Sorted by residual: chirality pdb=" C1' G B -36 " pdb=" O4' G B -36 " pdb=" C2' G B -36 " pdb=" N9 G B -36 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" C3' C B 1 " pdb=" C4' C B 1 " pdb=" O3' C B 1 " pdb=" C2' C B 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" C2' U B -6 " pdb=" C3' U B -6 " pdb=" O2' U B -6 " pdb=" C1' U B -6 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 1004 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 466 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 467 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 4 " -0.017 2.00e-02 2.50e+03 1.38e-02 4.73e+00 pdb=" CG TRP C 4 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 4 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 4 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 4 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 4 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 4 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 4 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 352 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ASP A 352 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A 352 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A 353 " 0.011 2.00e-02 2.50e+03 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1110 2.77 - 3.30: 6169 3.30 - 3.83: 10678 3.83 - 4.37: 12073 4.37 - 4.90: 19987 Nonbonded interactions: 50017 Sorted by model distance: nonbonded pdb=" OD1 ASN A 797 " pdb=" OH TYR A 852 " model vdw 2.232 3.040 nonbonded pdb=" O LYS A 579 " pdb=" O2' A B -21 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASP A 900 " pdb=" OG SER A 930 " model vdw 2.252 3.040 nonbonded pdb=" O2' A B -29 " pdb=" O4' A B -28 " model vdw 2.256 3.040 nonbonded pdb=" N4 C B -30 " pdb=" O6 G B -11 " model vdw 2.258 3.120 ... (remaining 50012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.710 Find NCS groups from input model: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 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 : 0.003 0.039 6521 Z= 0.161 Angle : 0.644 8.472 8962 Z= 0.369 Chirality : 0.042 0.184 1007 Planarity : 0.004 0.065 997 Dihedral : 21.100 172.743 2683 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.44 % Favored : 94.09 % Rotamer: Outliers : 1.15 % Allowed : 29.51 % Favored : 69.34 % 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: -1.33 (0.33), residues: 643 helix: 0.48 (0.33), residues: 258 sheet: -1.15 (0.56), residues: 76 loop : -2.05 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 542 TYR 0.018 0.001 TYR A 925 PHE 0.018 0.001 PHE A 234 TRP 0.037 0.003 TRP C 4 HIS 0.007 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6521) covalent geometry : angle 0.64368 ( 8962) hydrogen bonds : bond 0.20070 ( 239) hydrogen bonds : angle 6.90484 ( 665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.237 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 0.0660 time to fit residues: 5.7651 Evaluate side-chains 54 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 218 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 701 HIS A 763 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.156206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.141573 restraints weight = 17397.276| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.60 r_work: 0.4062 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6521 Z= 0.129 Angle : 0.592 6.496 8962 Z= 0.313 Chirality : 0.040 0.190 1007 Planarity : 0.004 0.051 997 Dihedral : 19.144 167.642 1305 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.51 % Favored : 95.33 % Rotamer: Outliers : 3.77 % Allowed : 25.74 % Favored : 70.49 % 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 (0.33), residues: 643 helix: 0.58 (0.33), residues: 262 sheet: -1.44 (0.54), residues: 88 loop : -1.93 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.012 0.001 TYR A 536 PHE 0.021 0.001 PHE A 234 TRP 0.027 0.002 TRP C 4 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6521) covalent geometry : angle 0.59151 ( 8962) hydrogen bonds : bond 0.04565 ( 239) hydrogen bonds : angle 5.27844 ( 665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.233 Fit side-chains REVERT: C 4 TRP cc_start: 0.6516 (p-90) cc_final: 0.6295 (p-90) REVERT: A 762 LEU cc_start: 0.1154 (OUTLIER) cc_final: 0.0918 (tt) outliers start: 23 outliers final: 13 residues processed: 72 average time/residue: 0.0633 time to fit residues: 6.6045 Evaluate side-chains 61 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN A 479 GLN ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** 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 = 0.4348 r_free = 0.4348 target = 0.150524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.135819 restraints weight = 17451.556| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.53 r_work: 0.3985 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6521 Z= 0.213 Angle : 0.667 6.972 8962 Z= 0.358 Chirality : 0.043 0.177 1007 Planarity : 0.004 0.048 997 Dihedral : 19.216 161.781 1303 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 4.92 % Allowed : 25.90 % Favored : 69.18 % 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: -1.54 (0.32), residues: 643 helix: 0.19 (0.32), residues: 262 sheet: -1.20 (0.58), residues: 83 loop : -2.10 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.018 0.002 TYR A 885 PHE 0.027 0.002 PHE A 234 TRP 0.016 0.002 TRP A 264 HIS 0.007 0.002 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 6521) covalent geometry : angle 0.66719 ( 8962) hydrogen bonds : bond 0.04853 ( 239) hydrogen bonds : angle 5.30923 ( 665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.235 Fit side-chains REVERT: C 4 TRP cc_start: 0.6766 (p-90) cc_final: 0.6495 (p-90) REVERT: A 448 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7222 (mm-30) REVERT: A 762 LEU cc_start: 0.1241 (OUTLIER) cc_final: 0.1011 (tt) REVERT: A 778 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6317 (p0) outliers start: 30 outliers final: 19 residues processed: 75 average time/residue: 0.0574 time to fit residues: 6.3597 Evaluate side-chains 66 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 701 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.152811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.137944 restraints weight = 17535.053| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 3.67 r_work: 0.4015 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6521 Z= 0.135 Angle : 0.595 8.288 8962 Z= 0.313 Chirality : 0.040 0.204 1007 Planarity : 0.004 0.046 997 Dihedral : 18.873 158.644 1301 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.35 % Favored : 95.33 % Rotamer: Outliers : 5.41 % Allowed : 26.07 % Favored : 68.52 % 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 (0.33), residues: 643 helix: 0.53 (0.32), residues: 262 sheet: -1.17 (0.58), residues: 82 loop : -1.96 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.015 0.001 TYR A 925 PHE 0.023 0.001 PHE A 234 TRP 0.017 0.002 TRP A 264 HIS 0.007 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6521) covalent geometry : angle 0.59520 ( 8962) hydrogen bonds : bond 0.03878 ( 239) hydrogen bonds : angle 4.95362 ( 665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 352 ASP cc_start: 0.7931 (t0) cc_final: 0.7730 (t0) REVERT: A 448 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 544 ILE cc_start: 0.5488 (OUTLIER) cc_final: 0.5013 (mt) REVERT: A 753 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.5974 (m-30) REVERT: A 762 LEU cc_start: 0.0869 (OUTLIER) cc_final: 0.0620 (tt) REVERT: A 778 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6317 (p0) outliers start: 33 outliers final: 23 residues processed: 76 average time/residue: 0.0557 time to fit residues: 6.2924 Evaluate side-chains 70 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.153231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.138455 restraints weight = 17502.827| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.58 r_work: 0.4018 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6521 Z= 0.125 Angle : 0.575 7.879 8962 Z= 0.302 Chirality : 0.040 0.199 1007 Planarity : 0.003 0.043 997 Dihedral : 18.579 158.714 1301 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.20 % Favored : 95.49 % Rotamer: Outliers : 5.90 % Allowed : 26.39 % Favored : 67.70 % 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: -1.07 (0.33), residues: 643 helix: 0.65 (0.33), residues: 262 sheet: -1.06 (0.59), residues: 82 loop : -1.87 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 416 TYR 0.012 0.001 TYR A 925 PHE 0.022 0.001 PHE A 234 TRP 0.017 0.001 TRP A 264 HIS 0.005 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6521) covalent geometry : angle 0.57520 ( 8962) hydrogen bonds : bond 0.03586 ( 239) hydrogen bonds : angle 4.79163 ( 665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 49 time to evaluate : 0.224 Fit side-chains REVERT: A 352 ASP cc_start: 0.8077 (t0) cc_final: 0.7845 (t0) REVERT: A 753 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.5985 (m-30) REVERT: A 762 LEU cc_start: 0.0808 (OUTLIER) cc_final: 0.0561 (tt) REVERT: A 778 ASN cc_start: 0.6777 (OUTLIER) cc_final: 0.6346 (p0) outliers start: 36 outliers final: 21 residues processed: 77 average time/residue: 0.0615 time to fit residues: 6.8243 Evaluate side-chains 66 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.154288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.139698 restraints weight = 17426.790| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.55 r_work: 0.4051 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6521 Z= 0.120 Angle : 0.578 8.409 8962 Z= 0.302 Chirality : 0.039 0.200 1007 Planarity : 0.003 0.041 997 Dihedral : 18.463 158.022 1301 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.89 % Favored : 95.80 % Rotamer: Outliers : 5.90 % Allowed : 27.05 % Favored : 67.05 % 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: -0.90 (0.33), residues: 643 helix: 0.78 (0.33), residues: 262 sheet: -0.80 (0.63), residues: 78 loop : -1.82 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 416 TYR 0.012 0.001 TYR A 925 PHE 0.023 0.001 PHE A 645 TRP 0.025 0.002 TRP A 264 HIS 0.008 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6521) covalent geometry : angle 0.57777 ( 8962) hydrogen bonds : bond 0.03395 ( 239) hydrogen bonds : angle 4.67865 ( 665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 43 time to evaluate : 0.201 Fit side-chains REVERT: A 352 ASP cc_start: 0.8118 (t0) cc_final: 0.7849 (t0) REVERT: A 423 ILE cc_start: 0.3823 (OUTLIER) cc_final: 0.3539 (tt) REVERT: A 753 ASP cc_start: 0.6465 (OUTLIER) cc_final: 0.5991 (m-30) REVERT: A 762 LEU cc_start: 0.0466 (OUTLIER) cc_final: 0.0222 (tt) REVERT: A 778 ASN cc_start: 0.6730 (OUTLIER) cc_final: 0.6309 (p0) outliers start: 36 outliers final: 25 residues processed: 72 average time/residue: 0.0458 time to fit residues: 5.1740 Evaluate side-chains 73 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 0.0870 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.154664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.140168 restraints weight = 17098.147| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.51 r_work: 0.4064 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6521 Z= 0.115 Angle : 0.567 8.983 8962 Z= 0.295 Chirality : 0.039 0.191 1007 Planarity : 0.003 0.040 997 Dihedral : 18.338 157.927 1301 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.20 % Favored : 95.49 % Rotamer: Outliers : 5.74 % Allowed : 26.89 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.33), residues: 643 helix: 0.77 (0.32), residues: 266 sheet: -0.75 (0.63), residues: 78 loop : -1.81 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.016 0.001 TYR A 925 PHE 0.020 0.001 PHE A 234 TRP 0.024 0.002 TRP A 264 HIS 0.006 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6521) covalent geometry : angle 0.56655 ( 8962) hydrogen bonds : bond 0.03335 ( 239) hydrogen bonds : angle 4.66453 ( 665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 45 time to evaluate : 0.153 Fit side-chains REVERT: A 294 GLN cc_start: 0.4145 (OUTLIER) cc_final: 0.3796 (mt0) REVERT: A 352 ASP cc_start: 0.8161 (t0) cc_final: 0.7881 (t0) REVERT: A 423 ILE cc_start: 0.3853 (OUTLIER) cc_final: 0.3590 (tt) REVERT: A 634 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6714 (p90) REVERT: A 753 ASP cc_start: 0.6440 (OUTLIER) cc_final: 0.5944 (m-30) REVERT: A 762 LEU cc_start: 0.0637 (OUTLIER) cc_final: 0.0378 (tt) REVERT: A 778 ASN cc_start: 0.6767 (OUTLIER) cc_final: 0.6331 (p0) outliers start: 35 outliers final: 25 residues processed: 72 average time/residue: 0.0463 time to fit residues: 5.2686 Evaluate side-chains 72 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 41 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.152608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.138061 restraints weight = 17360.782| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.49 r_work: 0.4023 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6521 Z= 0.151 Angle : 0.595 9.399 8962 Z= 0.313 Chirality : 0.041 0.181 1007 Planarity : 0.003 0.038 997 Dihedral : 18.368 160.373 1301 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.82 % Favored : 94.87 % Rotamer: Outliers : 5.57 % Allowed : 26.23 % Favored : 68.20 % 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: -0.87 (0.33), residues: 643 helix: 0.65 (0.32), residues: 265 sheet: -0.48 (0.62), residues: 76 loop : -1.76 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.026 0.002 TYR A 925 PHE 0.022 0.001 PHE A 234 TRP 0.032 0.002 TRP A 264 HIS 0.006 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6521) covalent geometry : angle 0.59513 ( 8962) hydrogen bonds : bond 0.03672 ( 239) hydrogen bonds : angle 4.78375 ( 665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 44 time to evaluate : 0.231 Fit side-chains REVERT: A 352 ASP cc_start: 0.8251 (t0) cc_final: 0.7969 (t0) REVERT: A 423 ILE cc_start: 0.3941 (OUTLIER) cc_final: 0.3724 (tt) REVERT: A 448 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 634 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6740 (p90) REVERT: A 753 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.5998 (m-30) REVERT: A 762 LEU cc_start: 0.0860 (OUTLIER) cc_final: 0.0598 (tt) REVERT: A 778 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6380 (p0) outliers start: 34 outliers final: 25 residues processed: 73 average time/residue: 0.0532 time to fit residues: 5.8412 Evaluate side-chains 71 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 41 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 859 LYS Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.146774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.132183 restraints weight = 18215.096| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.58 r_work: 0.3938 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6521 Z= 0.271 Angle : 0.759 9.024 8962 Z= 0.403 Chirality : 0.046 0.196 1007 Planarity : 0.004 0.035 997 Dihedral : 18.877 163.900 1301 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.93 % Rotamer: Outliers : 5.41 % Allowed : 27.21 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.32), residues: 643 helix: -0.20 (0.32), residues: 265 sheet: -1.12 (0.61), residues: 77 loop : -2.05 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 259 TYR 0.025 0.002 TYR A 885 PHE 0.028 0.002 PHE A 234 TRP 0.041 0.004 TRP A 264 HIS 0.007 0.002 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 6521) covalent geometry : angle 0.75920 ( 8962) hydrogen bonds : bond 0.05128 ( 239) hydrogen bonds : angle 5.61971 ( 665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 43 time to evaluate : 0.242 Fit side-chains REVERT: A 352 ASP cc_start: 0.8583 (t0) cc_final: 0.8343 (t0) REVERT: A 753 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6081 (m-30) REVERT: A 762 LEU cc_start: 0.1008 (OUTLIER) cc_final: 0.0717 (tt) outliers start: 33 outliers final: 24 residues processed: 70 average time/residue: 0.0454 time to fit residues: 5.0157 Evaluate side-chains 67 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 859 LYS Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.154606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.140189 restraints weight = 17528.548| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.55 r_work: 0.4031 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6521 Z= 0.128 Angle : 0.621 8.855 8962 Z= 0.323 Chirality : 0.041 0.254 1007 Planarity : 0.004 0.038 997 Dihedral : 18.507 159.025 1301 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.58 % Favored : 96.11 % Rotamer: Outliers : 3.77 % Allowed : 28.20 % Favored : 68.03 % 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: -1.25 (0.33), residues: 643 helix: 0.38 (0.32), residues: 268 sheet: -1.14 (0.64), residues: 72 loop : -1.90 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.020 0.001 TYR A 925 PHE 0.020 0.001 PHE A 234 TRP 0.038 0.002 TRP A 264 HIS 0.006 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6521) covalent geometry : angle 0.62061 ( 8962) hydrogen bonds : bond 0.03607 ( 239) hydrogen bonds : angle 5.01756 ( 665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 352 ASP cc_start: 0.8457 (t0) cc_final: 0.8171 (t0) REVERT: A 448 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 634 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6711 (p90) REVERT: A 690 MET cc_start: 0.8053 (tpp) cc_final: 0.7387 (tpp) REVERT: A 753 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6093 (m-30) REVERT: A 762 LEU cc_start: 0.0210 (OUTLIER) cc_final: -0.0038 (tt) REVERT: A 778 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6220 (p0) outliers start: 23 outliers final: 16 residues processed: 68 average time/residue: 0.0598 time to fit residues: 6.1248 Evaluate side-chains 63 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.0170 chunk 39 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.151076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.136438 restraints weight = 17739.307| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.55 r_work: 0.4008 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6521 Z= 0.146 Angle : 0.623 8.628 8962 Z= 0.324 Chirality : 0.041 0.231 1007 Planarity : 0.004 0.038 997 Dihedral : 18.482 161.486 1301 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.35 % Favored : 95.33 % Rotamer: Outliers : 3.28 % Allowed : 28.20 % Favored : 68.52 % 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: -1.19 (0.33), residues: 643 helix: 0.44 (0.32), residues: 269 sheet: -0.99 (0.63), residues: 77 loop : -1.92 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.022 0.001 TYR A 925 PHE 0.023 0.001 PHE A 234 TRP 0.051 0.002 TRP A 264 HIS 0.006 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6521) covalent geometry : angle 0.62345 ( 8962) hydrogen bonds : bond 0.03796 ( 239) hydrogen bonds : angle 4.99660 ( 665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1517.59 seconds wall clock time: 26 minutes 44.19 seconds (1604.19 seconds total)