Starting phenix.real_space_refine on Thu Jul 2 04:07:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ix6_60965/07_2026/9ix6_60965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ix6_60965/07_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_60965/07_2026/9ix6_60965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ix6_60965/07_2026/9ix6_60965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ix6_60965/07_2026/9ix6_60965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ix6_60965/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.03, per 1000 atoms: 0.16 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: 0.49 Conformation dependent library (CDL) restraints added in 187.7 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: 0.40 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: 0.83 Time building geometry restraints manager: 0.62 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=" N9 G B -4 " pdb=" C4 G B -4 " ideal model delta sigma weight residual 1.375 1.388 -0.013 8.00e-03 1.56e+04 2.78e+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=" C1' G B -36 " pdb=" N9 G B -36 " pdb=" C4 G B -36 " ideal model delta sigma weight residual 126.50 132.05 -5.55 1.30e+00 5.92e-01 1.82e+01 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=" N9 G B -36 " pdb=" C4 G B -36 " pdb=" N3 G B -36 " ideal model delta sigma weight residual 126.00 128.49 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" C1' G B -4 " pdb=" N9 G B -4 " pdb=" C4 G B -4 " ideal model delta sigma weight residual 126.50 131.86 -5.36 1.30e+00 5.92e-01 1.70e+01 angle pdb=" C1' G B -36 " pdb=" N9 G B -36 " pdb=" C8 G B -36 " ideal model delta sigma weight residual 127.00 121.87 5.13 1.30e+00 5.92e-01 1.56e+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: 3.810 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 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= 0.174 Angle : 0.644 8.472 8962 Z= 0.422 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/Z covalent geometry : bond 0.00298 / 0.17 ( 6521) covalent geometry : angle 0.64372 / 0.42 ( 8962) hydrogen bonds : bond 0.20070 / 13.18 ( 239) hydrogen bonds : angle 6.90484 / 4.84 ( 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 : 0.228 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 0.0485 time to fit residues: 4.2427 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 : 0.171 ------------------------------------------------------------------------------- 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... A 217 ASN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4428 r_free = 0.4428 target = 0.156413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.141695 restraints weight = 17434.701| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.60 r_work: 0.4070 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.0872 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= 0.138 Angle : 0.583 6.061 8962 Z= 0.331 Chirality : 0.041 0.212 1007 Planarity : 0.004 0.050 997 Dihedral : 19.324 170.986 1305 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.18 % Rotamer: Outliers : 3.93 % Allowed : 25.90 % Favored : 70.16 % 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: -1.29 (0.33), residues: 643 helix: 0.44 (0.32), residues: 266 sheet: -1.47 (0.54), residues: 89 loop : -1.91 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.013 0.001 TYR A 536 PHE 0.021 0.001 PHE A 234 TRP 0.030 0.002 TRP C 4 HIS 0.003 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 6521) covalent geometry : angle 0.58298 / 0.33 ( 8962) hydrogen bonds : bond 0.05072 / 3.07 ( 239) hydrogen bonds : angle 5.54057 / 3.99 ( 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: 24 poor density : 54 time to evaluate : 0.151 Fit side-chains REVERT: C 4 TRP cc_start: 0.6285 (p-90) cc_final: 0.6055 (p-90) REVERT: A 762 LEU cc_start: 0.1265 (OUTLIER) cc_final: 0.1028 (tt) outliers start: 24 outliers final: 13 residues processed: 73 average time/residue: 0.0469 time to fit residues: 5.0509 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 : 0.168 ------------------------------------------------------------------------------- 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 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 884 SER 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: 2.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 835 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.150378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.135365 restraints weight = 17699.352| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.68 r_work: 0.3976 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6521 Z= 0.257 Angle : 0.682 7.163 8962 Z= 0.384 Chirality : 0.046 0.184 1007 Planarity : 0.005 0.048 997 Dihedral : 19.278 162.819 1303 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.84 % Favored : 93.00 % Rotamer: Outliers : 5.25 % Allowed : 25.90 % Favored : 68.85 % 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: -1.76 (0.31), residues: 643 helix: -0.07 (0.31), residues: 262 sheet: -1.22 (0.57), residues: 79 loop : -2.17 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 267 TYR 0.020 0.002 TYR A 885 PHE 0.028 0.002 PHE A 234 TRP 0.027 0.003 TRP A 264 HIS 0.005 0.002 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 ( 6521) covalent geometry : angle 0.68163 / 0.38 ( 8962) hydrogen bonds : bond 0.05574 / 3.39 ( 239) hydrogen bonds : angle 5.54093 / 4.04 ( 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 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 0.220 Fit side-chains REVERT: C 4 TRP cc_start: 0.6852 (p-90) cc_final: 0.6539 (p-90) REVERT: A 431 ARG cc_start: 0.8661 (mmm160) cc_final: 0.8446 (mmm160) REVERT: A 778 ASN cc_start: 0.7062 (OUTLIER) cc_final: 0.6498 (p0) outliers start: 32 outliers final: 19 residues processed: 77 average time/residue: 0.0492 time to fit residues: 5.4995 Evaluate side-chains 66 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE 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 747 SER Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 764 SER 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 877 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 884 SER 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: 1.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN A 479 GLN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.153575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.138795 restraints weight = 17751.872| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.60 r_work: 0.4030 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.1688 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= 0.137 Angle : 0.591 7.750 8962 Z= 0.322 Chirality : 0.041 0.215 1007 Planarity : 0.004 0.046 997 Dihedral : 19.122 164.920 1301 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.82 % Favored : 95.02 % Rotamer: Outliers : 5.57 % Allowed : 25.74 % Favored : 68.69 % 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: -1.42 (0.32), residues: 643 helix: 0.33 (0.32), residues: 262 sheet: -1.23 (0.57), residues: 83 loop : -2.04 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.014 0.002 TYR A 406 PHE 0.022 0.001 PHE A 234 TRP 0.017 0.002 TRP C 4 HIS 0.005 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 6521) covalent geometry : angle 0.59074 / 0.32 ( 8962) hydrogen bonds : bond 0.04305 / 2.64 ( 239) hydrogen bonds : angle 5.19470 / 3.79 ( 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 82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 48 time to evaluate : 0.147 Fit side-chains REVERT: A 717 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.5776 (p0) REVERT: A 778 ASN cc_start: 0.6892 (OUTLIER) cc_final: 0.6268 (p0) outliers start: 34 outliers final: 23 residues processed: 73 average time/residue: 0.0480 time to fit residues: 5.1973 Evaluate side-chains 69 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 384 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 527 VAL 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 717 ASN Chi-restraints excluded: chain A residue 747 SER 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 889 THR 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: 0.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN A 429 GLN ** A 631 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 = 0.4379 r_free = 0.4379 target = 0.152831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.138040 restraints weight = 17694.505| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.62 r_work: 0.4024 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.1846 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= 0.138 Angle : 0.563 7.241 8962 Z= 0.314 Chirality : 0.040 0.210 1007 Planarity : 0.003 0.043 997 Dihedral : 19.009 163.446 1301 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.82 % Favored : 94.87 % Rotamer: Outliers : 5.74 % Allowed : 26.39 % Favored : 67.87 % 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: -1.31 (0.33), residues: 643 helix: 0.41 (0.32), residues: 262 sheet: -1.18 (0.60), residues: 82 loop : -1.97 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.014 0.001 TYR A 885 PHE 0.023 0.001 PHE A 234 TRP 0.043 0.002 TRP C 4 HIS 0.005 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 6521) covalent geometry : angle 0.56277 / 0.31 ( 8962) hydrogen bonds : bond 0.04060 / 2.49 ( 239) hydrogen bonds : angle 5.07675 / 3.70 ( 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: 35 poor density : 50 time to evaluate : 0.197 Fit side-chains REVERT: A 544 ILE cc_start: 0.5488 (OUTLIER) cc_final: 0.5001 (mt) REVERT: A 753 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.6026 (m-30) REVERT: A 778 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6388 (p0) outliers start: 35 outliers final: 28 residues processed: 75 average time/residue: 0.0542 time to fit residues: 5.8476 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 499 ASP 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 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 733 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 ASP 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 889 THR 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: 0.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 GLN A 763 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.153561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.139086 restraints weight = 17572.058| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 3.54 r_work: 0.4038 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6521 Z= 0.121 Angle : 0.568 9.868 8962 Z= 0.308 Chirality : 0.040 0.214 1007 Planarity : 0.004 0.041 997 Dihedral : 18.908 164.459 1301 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.35 % Favored : 95.33 % Rotamer: Outliers : 6.23 % Allowed : 26.07 % 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: -1.18 (0.33), residues: 643 helix: 0.60 (0.33), residues: 260 sheet: -1.16 (0.59), residues: 82 loop : -1.94 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 431 TYR 0.014 0.001 TYR A 857 PHE 0.022 0.001 PHE A 234 TRP 0.029 0.002 TRP C 4 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6521) covalent geometry : angle 0.56823 / 0.31 ( 8962) hydrogen bonds : bond 0.03760 / 2.31 ( 239) hydrogen bonds : angle 4.94719 / 3.61 ( 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 90 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 52 time to evaluate : 0.138 Fit side-chains REVERT: A 753 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.6039 (m-30) REVERT: A 778 ASN cc_start: 0.6680 (OUTLIER) cc_final: 0.6315 (p0) outliers start: 38 outliers final: 27 residues processed: 80 average time/residue: 0.0447 time to fit residues: 5.3257 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 : 0.179 ------------------------------------------------------------------------------- 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 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 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 749 CYS Chi-restraints excluded: chain A residue 753 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.150609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.136084 restraints weight = 17536.777| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 3.52 r_work: 0.3994 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6521 Z= 0.202 Angle : 0.620 8.581 8962 Z= 0.342 Chirality : 0.042 0.198 1007 Planarity : 0.004 0.039 997 Dihedral : 18.925 161.332 1301 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.93 % Rotamer: Outliers : 6.23 % Allowed : 25.41 % Favored : 68.36 % 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: -1.41 (0.33), residues: 643 helix: 0.27 (0.32), residues: 263 sheet: -1.21 (0.59), residues: 82 loop : -1.97 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 431 TYR 0.017 0.002 TYR A 885 PHE 0.025 0.002 PHE A 234 TRP 0.017 0.002 TRP C 4 HIS 0.004 0.001 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 6521) covalent geometry : angle 0.61971 / 0.34 ( 8962) hydrogen bonds : bond 0.04315 / 2.65 ( 239) hydrogen bonds : angle 5.15240 / 3.77 ( 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 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 45 time to evaluate : 0.163 Fit side-chains REVERT: A 352 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8019 (t0) REVERT: A 753 ASP cc_start: 0.6532 (OUTLIER) cc_final: 0.6013 (m-30) REVERT: A 778 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6370 (p0) outliers start: 38 outliers final: 31 residues processed: 74 average time/residue: 0.0420 time to fit residues: 4.9595 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 43 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 352 ASP 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 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 609 PHE Chi-restraints excluded: chain A residue 612 LEU 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 733 VAL Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 764 SER 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 889 THR 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: 0.8980 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** 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 = 0.4387 r_free = 0.4387 target = 0.153028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.138582 restraints weight = 17577.410| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.51 r_work: 0.4038 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2203 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= 0.119 Angle : 0.563 8.907 8962 Z= 0.308 Chirality : 0.040 0.216 1007 Planarity : 0.004 0.038 997 Dihedral : 18.755 162.819 1301 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.04 % Favored : 95.65 % Rotamer: Outliers : 5.41 % Allowed : 26.56 % 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: -1.13 (0.33), residues: 643 helix: 0.53 (0.32), residues: 262 sheet: -1.06 (0.60), residues: 82 loop : -1.84 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 431 TYR 0.012 0.001 TYR A 885 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/Z covalent geometry : bond 0.00252 / 0.12 ( 6521) covalent geometry : angle 0.56260 / 0.31 ( 8962) hydrogen bonds : bond 0.03665 / 2.25 ( 239) hydrogen bonds : angle 4.94646 / 3.61 ( 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: 33 poor density : 45 time to evaluate : 0.139 Fit side-chains REVERT: A 352 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7933 (t0) REVERT: A 448 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6745 (mm-30) REVERT: A 753 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.5975 (m-30) REVERT: A 778 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6302 (p0) outliers start: 33 outliers final: 29 residues processed: 69 average time/residue: 0.0431 time to fit residues: 4.6216 Evaluate side-chains 75 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 43 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 352 ASP 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 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 609 PHE Chi-restraints excluded: chain A residue 612 LEU 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 749 CYS Chi-restraints excluded: chain A residue 753 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** 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 = 0.4385 r_free = 0.4385 target = 0.152778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.138326 restraints weight = 17683.013| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.51 r_work: 0.4035 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.2312 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= 0.123 Angle : 0.568 9.204 8962 Z= 0.307 Chirality : 0.040 0.205 1007 Planarity : 0.004 0.045 997 Dihedral : 18.588 161.719 1301 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.51 % Favored : 95.18 % Rotamer: Outliers : 4.92 % Allowed : 26.89 % 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: -1.00 (0.33), residues: 643 helix: 0.53 (0.32), residues: 262 sheet: -0.63 (0.59), residues: 80 loop : -1.78 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 431 TYR 0.013 0.001 TYR A 857 PHE 0.022 0.001 PHE A 234 TRP 0.023 0.002 TRP C 4 HIS 0.005 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6521) covalent geometry : angle 0.56778 / 0.31 ( 8962) hydrogen bonds : bond 0.03560 / 2.21 ( 239) hydrogen bonds : angle 4.86130 / 3.55 ( 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 74 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 0.139 Fit side-chains REVERT: A 352 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8000 (t0) REVERT: A 448 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6765 (mm-30) REVERT: A 753 ASP cc_start: 0.6479 (OUTLIER) cc_final: 0.6007 (m-30) REVERT: A 778 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6340 (p0) outliers start: 30 outliers final: 25 residues processed: 66 average time/residue: 0.0393 time to fit residues: 4.0401 Evaluate side-chains 71 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 352 ASP 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 575 VAL Chi-restraints excluded: chain A residue 612 LEU 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 749 CYS Chi-restraints excluded: chain A residue 753 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.151875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.137432 restraints weight = 17383.229| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.50 r_work: 0.4021 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6521 Z= 0.143 Angle : 0.575 9.216 8962 Z= 0.313 Chirality : 0.041 0.200 1007 Planarity : 0.004 0.042 997 Dihedral : 18.577 160.036 1301 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.67 % Favored : 95.02 % Rotamer: Outliers : 4.92 % Allowed : 27.21 % Favored : 67.87 % 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: -1.06 (0.33), residues: 643 helix: 0.44 (0.32), residues: 262 sheet: -0.46 (0.62), residues: 76 loop : -1.81 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 431 TYR 0.014 0.001 TYR A 885 PHE 0.022 0.001 PHE A 234 TRP 0.016 0.002 TRP A 244 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6521) covalent geometry : angle 0.57546 / 0.31 ( 8962) hydrogen bonds : bond 0.03732 / 2.30 ( 239) hydrogen bonds : angle 4.90954 / 3.59 ( 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 73 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 0.137 Fit side-chains REVERT: A 423 ILE cc_start: 0.3826 (OUTLIER) cc_final: 0.3584 (tt) REVERT: A 753 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6048 (m-30) REVERT: A 778 ASN cc_start: 0.6840 (OUTLIER) cc_final: 0.6325 (p0) outliers start: 30 outliers final: 25 residues processed: 66 average time/residue: 0.0364 time to fit residues: 3.9207 Evaluate side-chains 71 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 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 609 PHE Chi-restraints excluded: chain A residue 612 LEU 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 749 CYS Chi-restraints excluded: chain A residue 753 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** 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 = 0.4376 r_free = 0.4376 target = 0.152226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.137902 restraints weight = 17508.433| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.50 r_work: 0.4025 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6521 Z= 0.130 Angle : 0.565 9.143 8962 Z= 0.309 Chirality : 0.040 0.201 1007 Planarity : 0.004 0.041 997 Dihedral : 18.550 159.884 1301 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.82 % Favored : 94.87 % Rotamer: Outliers : 5.25 % Allowed : 26.72 % 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: -1.02 (0.33), residues: 643 helix: 0.49 (0.32), residues: 262 sheet: -0.43 (0.62), residues: 76 loop : -1.82 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 431 TYR 0.013 0.001 TYR A 885 PHE 0.022 0.001 PHE A 234 TRP 0.018 0.002 TRP C 4 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6521) covalent geometry : angle 0.56539 / 0.31 ( 8962) hydrogen bonds : bond 0.03615 / 2.23 ( 239) hydrogen bonds : angle 4.87614 / 3.57 ( 665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.16 seconds wall clock time: 21 minutes 19.83 seconds (1279.83 seconds total)