Starting phenix.real_space_refine on Wed Mar 4 14:23:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o6b_12737/03_2026/7o6b_12737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o6b_12737/03_2026/7o6b_12737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o6b_12737/03_2026/7o6b_12737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o6b_12737/03_2026/7o6b_12737.map" model { file = "/net/cci-nas-00/data/ceres_data/7o6b_12737/03_2026/7o6b_12737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o6b_12737/03_2026/7o6b_12737.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 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 S 18 5.16 5 C 4543 2.51 5 N 1206 2.21 5 O 1393 1.98 5 H 7040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 14200 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 14200 Classifications: {'peptide': 879} Link IDs: {'PTRANS': 35, 'TRANS': 843} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.38, per 1000 atoms: 0.17 Number of scatterers: 14200 At special positions: 0 Unit cell: (68.724, 120.888, 126.684, 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 18 16.00 O 1393 8.00 N 1206 7.00 C 4543 6.00 H 7040 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1160 " distance=2.03 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: 0.99 Conformation dependent library (CDL) restraints added in 309.8 milliseconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 61.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 340 through 360 Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.809A pdb=" N PHE A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.762A pdb=" N SER A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 442 removed outlier: 3.869A pdb=" N GLU A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 466 through 477 Processing helix chain 'A' and resid 510 through 516 removed outlier: 4.167A pdb=" N VAL A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.592A pdb=" N VAL A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 4.025A pdb=" N ASN A 554 " --> pdb=" O GLU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.825A pdb=" N SER A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 600 removed outlier: 3.972A pdb=" N LYS A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 removed outlier: 4.180A pdb=" N ASP A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 637 through 650 removed outlier: 4.269A pdb=" N PHE A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.637A pdb=" N LEU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 672 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 734 removed outlier: 3.838A pdb=" N GLN A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 807 removed outlier: 4.127A pdb=" N PHE A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 835 removed outlier: 3.941A pdb=" N LYS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 Processing helix chain 'A' and resid 860 through 867 removed outlier: 3.573A pdb=" N ALA A 864 " --> pdb=" O SER A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 886 Processing helix chain 'A' and resid 886 through 894 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 912 through 931 removed outlier: 3.541A pdb=" N ALA A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 939 Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 947 through 951 Processing helix chain 'A' and resid 955 through 970 removed outlier: 3.713A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 986 through 994 Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1022 through 1024 No H-bonds generated for 'chain 'A' and resid 1022 through 1024' Processing helix chain 'A' and resid 1025 through 1037 Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1053 through 1063 removed outlier: 4.091A pdb=" N ILE A1057 " --> pdb=" O MET A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 Processing helix chain 'A' and resid 1074 through 1087 Processing helix chain 'A' and resid 1090 through 1101 Processing helix chain 'A' and resid 1117 through 1126 Processing helix chain 'A' and resid 1175 through 1179 removed outlier: 4.237A pdb=" N GLU A1178 " --> pdb=" O PRO A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1226 through 1240 removed outlier: 3.956A pdb=" N GLU A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A1236 " --> pdb=" O GLU A1232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AA2, first strand: chain 'A' and resid 776 through 782 removed outlier: 3.601A pdb=" N ARG A 778 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 766 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 812 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 811 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 933 through 934 removed outlier: 6.250A pdb=" N VAL A 933 " --> pdb=" O TYR A 998 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1136 through 1145 removed outlier: 6.857A pdb=" N ILE A1151 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU A1159 " --> pdb=" O ALA A1200 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A1202 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A1161 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A1199 " --> pdb=" O ILE A1193 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A1193 " --> pdb=" O THR A1199 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU A1201 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A1186 " --> pdb=" O VAL A1140 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7036 1.03 - 1.23: 131 1.23 - 1.43: 2981 1.43 - 1.63: 4165 1.63 - 1.83: 30 Bond restraints: 14343 Sorted by residual: bond pdb=" NH1 ARG A1141 " pdb="HH12 ARG A1141 " ideal model delta sigma weight residual 0.860 0.830 0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NH1 ARG A 957 " pdb="HH12 ARG A 957 " ideal model delta sigma weight residual 0.860 0.837 0.023 2.00e-02 2.50e+03 1.36e+00 bond pdb=" CG1 ILE A1044 " pdb=" CD1 ILE A1044 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.21e+00 bond pdb=" CG LEU A 642 " pdb=" CD2 LEU A 642 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.61e-01 bond pdb=" NH1 ARG A1066 " pdb="HH12 ARG A1066 " ideal model delta sigma weight residual 0.860 0.843 0.017 2.00e-02 2.50e+03 6.92e-01 ... (remaining 14338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 25517 1.73 - 3.46: 376 3.46 - 5.19: 30 5.19 - 6.92: 5 6.92 - 8.65: 2 Bond angle restraints: 25930 Sorted by residual: angle pdb=" N PRO A 541 " pdb=" CA PRO A 541 " pdb=" C PRO A 541 " ideal model delta sigma weight residual 112.47 121.12 -8.65 2.06e+00 2.36e-01 1.76e+01 angle pdb=" N SER A 542 " pdb=" CA SER A 542 " pdb=" C SER A 542 " ideal model delta sigma weight residual 114.12 119.78 -5.66 1.39e+00 5.18e-01 1.66e+01 angle pdb=" C SER A 542 " pdb=" N SER A 543 " pdb=" CA SER A 543 " ideal model delta sigma weight residual 122.33 117.20 5.13 1.68e+00 3.54e-01 9.31e+00 angle pdb=" N SER A 543 " pdb=" CA SER A 543 " pdb=" C SER A 543 " ideal model delta sigma weight residual 108.69 113.48 -4.79 1.77e+00 3.19e-01 7.33e+00 angle pdb=" N GLY A1117 " pdb=" CA GLY A1117 " pdb=" C GLY A1117 " ideal model delta sigma weight residual 113.18 119.18 -6.00 2.37e+00 1.78e-01 6.42e+00 ... (remaining 25925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6312 17.66 - 35.33: 342 35.33 - 52.99: 81 52.99 - 70.66: 27 70.66 - 88.32: 1 Dihedral angle restraints: 6763 sinusoidal: 3663 harmonic: 3100 Sorted by residual: dihedral pdb=" CB CYS A1152 " pdb=" SG CYS A1152 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual -86.00 -149.02 63.02 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CD ARG A1109 " pdb=" NE ARG A1109 " pdb=" CZ ARG A1109 " pdb=" NH1 ARG A1109 " ideal model delta sinusoidal sigma weight residual 0.00 32.83 -32.83 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CA ASP A 622 " pdb=" CB ASP A 622 " pdb=" CG ASP A 622 " pdb=" OD1 ASP A 622 " ideal model delta sinusoidal sigma weight residual -30.00 -85.26 55.26 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 6760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 865 0.047 - 0.093: 169 0.093 - 0.140: 47 0.140 - 0.186: 6 0.186 - 0.233: 1 Chirality restraints: 1088 Sorted by residual: chirality pdb=" CA PRO A 541 " pdb=" N PRO A 541 " pdb=" C PRO A 541 " pdb=" CB PRO A 541 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 818 " pdb=" N PRO A 818 " pdb=" C PRO A 818 " pdb=" CB PRO A 818 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 747 " pdb=" N ILE A 747 " pdb=" C ILE A 747 " pdb=" CB ILE A 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1085 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1141 " -0.060 9.50e-02 1.11e+02 6.21e-02 7.83e+01 pdb=" NE ARG A1141 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A1141 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A1141 " -0.103 2.00e-02 2.50e+03 pdb=" NH2 ARG A1141 " 0.056 2.00e-02 2.50e+03 pdb="HH11 ARG A1141 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A1141 " 0.109 2.00e-02 2.50e+03 pdb="HH21 ARG A1141 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1141 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 957 " 0.137 9.50e-02 1.11e+02 6.81e-02 5.95e+01 pdb=" NE ARG A 957 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 957 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG A 957 " -0.098 2.00e-02 2.50e+03 pdb=" NH2 ARG A 957 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG A 957 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 957 " 0.097 2.00e-02 2.50e+03 pdb="HH21 ARG A 957 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 957 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1109 " -0.495 9.50e-02 1.11e+02 1.67e-01 4.54e+01 pdb=" NE ARG A1109 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A1109 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A1109 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A1109 " 0.040 2.00e-02 2.50e+03 pdb="HH11 ARG A1109 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A1109 " 0.032 2.00e-02 2.50e+03 pdb="HH21 ARG A1109 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1109 " -0.042 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 219 2.04 - 2.68: 21803 2.68 - 3.32: 41829 3.32 - 3.96: 50574 3.96 - 4.60: 78866 Nonbonded interactions: 193291 Sorted by model distance: nonbonded pdb=" HG1 THR A 895 " pdb=" OE1 GLU A 898 " model vdw 1.401 2.450 nonbonded pdb=" OE2 GLU A 866 " pdb="HH22 ARG A 882 " model vdw 1.544 2.450 nonbonded pdb="HH11 ARG A 976 " pdb=" OH TYR A1026 " model vdw 1.573 2.450 nonbonded pdb=" O LYS A 749 " pdb=" H ASN A 809 " model vdw 1.584 2.450 nonbonded pdb=" H LEU A 974 " pdb=" OE1 GLN A 978 " model vdw 1.588 2.450 ... (remaining 193286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.040 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.720 Find NCS groups from input model: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 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 0.043 7304 Z= 0.129 Angle : 0.673 8.647 9881 Z= 0.401 Chirality : 0.042 0.233 1088 Planarity : 0.012 0.206 1290 Dihedral : 11.536 88.323 2758 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.38 % Allowed : 3.41 % Favored : 96.21 % 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 (0.27), residues: 865 helix: -0.17 (0.22), residues: 465 sheet: -1.36 (0.60), residues: 74 loop : -0.76 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.005 ARG A1109 TYR 0.028 0.006 TYR A 998 PHE 0.019 0.003 PHE A 407 TRP 0.025 0.006 TRP A 415 HIS 0.016 0.004 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7303) covalent geometry : angle 0.67246 ( 9879) SS BOND : bond 0.00029 ( 1) SS BOND : angle 2.57927 ( 2) hydrogen bonds : bond 0.14871 ( 366) hydrogen bonds : angle 7.04744 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLU cc_start: -0.4118 (OUTLIER) cc_final: -0.4857 (mt-10) REVERT: A 520 SER cc_start: 0.5776 (OUTLIER) cc_final: 0.5558 (p) REVERT: A 633 HIS cc_start: 0.6997 (m170) cc_final: 0.6633 (m170) REVERT: A 1144 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8551 (mmp80) REVERT: A 1157 GLU cc_start: 0.8492 (tt0) cc_final: 0.8148 (tp30) REVERT: A 1242 MET cc_start: 0.6620 (tpt) cc_final: 0.5613 (mtt) outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.2255 time to fit residues: 36.0022 Evaluate side-chains 80 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 642 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.135003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.106435 restraints weight = 78180.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.110124 restraints weight = 39049.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.112153 restraints weight = 24798.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.113265 restraints weight = 18896.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.113867 restraints weight = 16452.256| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7304 Z= 0.133 Angle : 0.573 9.589 9881 Z= 0.311 Chirality : 0.041 0.145 1088 Planarity : 0.005 0.050 1290 Dihedral : 4.448 49.198 958 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.01 % Allowed : 7.83 % Favored : 91.16 % 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: 0.35 (0.29), residues: 865 helix: 0.82 (0.23), residues: 472 sheet: -1.12 (0.65), residues: 72 loop : -0.15 (0.39), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 900 TYR 0.012 0.001 TYR A 876 PHE 0.013 0.002 PHE A1145 TRP 0.013 0.001 TRP A 918 HIS 0.004 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7303) covalent geometry : angle 0.57244 ( 9879) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.86700 ( 2) hydrogen bonds : bond 0.05242 ( 366) hydrogen bonds : angle 5.70192 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 ARG cc_start: 0.8928 (ttm110) cc_final: 0.8535 (mmm160) REVERT: A 1157 GLU cc_start: 0.8335 (tt0) cc_final: 0.7891 (tp30) REVERT: A 1192 TYR cc_start: 0.7330 (t80) cc_final: 0.7014 (t80) REVERT: A 1242 MET cc_start: 0.6710 (tpt) cc_final: 0.5824 (mtt) outliers start: 8 outliers final: 8 residues processed: 87 average time/residue: 0.1751 time to fit residues: 21.1963 Evaluate side-chains 88 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1044 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 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 = 0.4516 r_free = 0.4516 target = 0.132325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.104563 restraints weight = 80675.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.108330 restraints weight = 40944.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.110367 restraints weight = 25683.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.111675 restraints weight = 19345.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.112264 restraints weight = 16489.282| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7304 Z= 0.166 Angle : 0.542 7.326 9881 Z= 0.299 Chirality : 0.040 0.142 1088 Planarity : 0.004 0.046 1290 Dihedral : 4.317 48.630 954 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.14 % Allowed : 9.72 % Favored : 89.14 % 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: 0.22 (0.29), residues: 865 helix: 0.82 (0.23), residues: 478 sheet: -1.13 (0.65), residues: 69 loop : -0.45 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 629 TYR 0.010 0.001 TYR A1039 PHE 0.018 0.002 PHE A 424 TRP 0.005 0.001 TRP A1146 HIS 0.003 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7303) covalent geometry : angle 0.54217 ( 9879) SS BOND : bond 0.00404 ( 1) SS BOND : angle 0.79952 ( 2) hydrogen bonds : bond 0.04715 ( 366) hydrogen bonds : angle 5.57959 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 633 HIS cc_start: 0.6794 (m170) cc_final: 0.6571 (m170) REVERT: A 1144 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8520 (mmm160) REVERT: A 1192 TYR cc_start: 0.7453 (t80) cc_final: 0.7096 (t80) REVERT: A 1242 MET cc_start: 0.6726 (tpt) cc_final: 0.5782 (mtt) outliers start: 9 outliers final: 9 residues processed: 82 average time/residue: 0.1818 time to fit residues: 20.5095 Evaluate side-chains 85 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1044 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.131234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.104475 restraints weight = 80895.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.108104 restraints weight = 40459.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.110190 restraints weight = 25984.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.111350 restraints weight = 19540.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.111897 restraints weight = 16698.517| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7304 Z= 0.151 Angle : 0.524 6.777 9881 Z= 0.287 Chirality : 0.039 0.139 1088 Planarity : 0.004 0.043 1290 Dihedral : 4.439 51.403 954 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.64 % Allowed : 10.98 % Favored : 87.37 % 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: 0.11 (0.29), residues: 865 helix: 0.78 (0.23), residues: 481 sheet: -1.31 (0.66), residues: 61 loop : -0.58 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 629 TYR 0.014 0.001 TYR A 876 PHE 0.015 0.002 PHE A 424 TRP 0.004 0.001 TRP A1146 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7303) covalent geometry : angle 0.52381 ( 9879) SS BOND : bond 0.00300 ( 1) SS BOND : angle 0.63414 ( 2) hydrogen bonds : bond 0.04434 ( 366) hydrogen bonds : angle 5.46358 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 633 HIS cc_start: 0.6792 (m170) cc_final: 0.6572 (m170) REVERT: A 1144 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8497 (mmm160) REVERT: A 1192 TYR cc_start: 0.7473 (t80) cc_final: 0.7101 (t80) REVERT: A 1242 MET cc_start: 0.6772 (tpt) cc_final: 0.5831 (mtt) outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 0.1884 time to fit residues: 20.7227 Evaluate side-chains 87 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.131474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.104465 restraints weight = 82327.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.108208 restraints weight = 40806.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.110161 restraints weight = 25999.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.111246 restraints weight = 19918.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.111881 restraints weight = 17219.999| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7304 Z= 0.130 Angle : 0.505 6.771 9881 Z= 0.274 Chirality : 0.039 0.138 1088 Planarity : 0.004 0.040 1290 Dihedral : 4.427 52.858 954 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.77 % Allowed : 11.99 % Favored : 86.24 % 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: 0.25 (0.29), residues: 865 helix: 0.94 (0.23), residues: 481 sheet: -1.29 (0.67), residues: 61 loop : -0.59 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 629 TYR 0.012 0.001 TYR A 876 PHE 0.013 0.001 PHE A 424 TRP 0.004 0.001 TRP A1146 HIS 0.003 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7303) covalent geometry : angle 0.50514 ( 9879) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.51698 ( 2) hydrogen bonds : bond 0.04181 ( 366) hydrogen bonds : angle 5.27482 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8468 (mmm160) REVERT: A 1192 TYR cc_start: 0.7409 (t80) cc_final: 0.7060 (t80) REVERT: A 1242 MET cc_start: 0.6831 (tpt) cc_final: 0.5837 (mtt) outliers start: 14 outliers final: 14 residues processed: 82 average time/residue: 0.1978 time to fit residues: 21.8309 Evaluate side-chains 89 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 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 = 0.4506 r_free = 0.4506 target = 0.131508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.104084 restraints weight = 81347.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.107739 restraints weight = 40224.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.109642 restraints weight = 25697.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.110913 restraints weight = 19902.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.111395 restraints weight = 17039.115| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7304 Z= 0.128 Angle : 0.498 6.772 9881 Z= 0.270 Chirality : 0.039 0.137 1088 Planarity : 0.004 0.039 1290 Dihedral : 4.427 54.905 954 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.02 % Allowed : 11.99 % Favored : 85.98 % 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: 0.36 (0.29), residues: 865 helix: 1.12 (0.24), residues: 469 sheet: -1.44 (0.64), residues: 61 loop : -0.62 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.017 0.001 TYR A 891 PHE 0.013 0.001 PHE A 424 TRP 0.005 0.001 TRP A 415 HIS 0.003 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7303) covalent geometry : angle 0.49825 ( 9879) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.46139 ( 2) hydrogen bonds : bond 0.04022 ( 366) hydrogen bonds : angle 5.18676 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8479 (mmm160) REVERT: A 1192 TYR cc_start: 0.7442 (t80) cc_final: 0.7086 (t80) REVERT: A 1242 MET cc_start: 0.6804 (tpt) cc_final: 0.5862 (mtt) outliers start: 16 outliers final: 14 residues processed: 87 average time/residue: 0.1895 time to fit residues: 22.5245 Evaluate side-chains 89 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 69 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.130966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.104342 restraints weight = 81414.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.108069 restraints weight = 40455.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.110048 restraints weight = 25656.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.111125 restraints weight = 19591.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.111807 restraints weight = 16869.683| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7304 Z= 0.129 Angle : 0.496 6.737 9881 Z= 0.269 Chirality : 0.039 0.138 1088 Planarity : 0.004 0.040 1290 Dihedral : 4.470 57.356 954 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.77 % Allowed : 12.75 % Favored : 85.48 % 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: 0.37 (0.29), residues: 865 helix: 1.12 (0.24), residues: 471 sheet: -1.38 (0.66), residues: 61 loop : -0.60 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.011 0.001 TYR A 891 PHE 0.012 0.001 PHE A 424 TRP 0.007 0.001 TRP A 415 HIS 0.003 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7303) covalent geometry : angle 0.49612 ( 9879) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.43031 ( 2) hydrogen bonds : bond 0.03945 ( 366) hydrogen bonds : angle 5.12495 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 ARG cc_start: 0.8890 (ttm110) cc_final: 0.8460 (mmm160) REVERT: A 1192 TYR cc_start: 0.7515 (t80) cc_final: 0.7171 (t80) REVERT: A 1242 MET cc_start: 0.6828 (tpt) cc_final: 0.5861 (mtt) outliers start: 14 outliers final: 14 residues processed: 83 average time/residue: 0.2001 time to fit residues: 22.4978 Evaluate side-chains 87 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 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 = 0.4492 r_free = 0.4492 target = 0.130417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.103471 restraints weight = 83141.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.107156 restraints weight = 42059.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.109178 restraints weight = 26665.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.110239 restraints weight = 20362.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.110918 restraints weight = 17497.364| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7304 Z= 0.141 Angle : 0.505 6.717 9881 Z= 0.275 Chirality : 0.039 0.138 1088 Planarity : 0.004 0.041 1290 Dihedral : 4.530 59.137 954 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.02 % Allowed : 12.63 % Favored : 85.35 % 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: 0.33 (0.29), residues: 865 helix: 1.12 (0.24), residues: 469 sheet: -1.44 (0.65), residues: 61 loop : -0.65 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 900 TYR 0.013 0.001 TYR A 891 PHE 0.013 0.001 PHE A 424 TRP 0.007 0.001 TRP A 415 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7303) covalent geometry : angle 0.50549 ( 9879) SS BOND : bond 0.00215 ( 1) SS BOND : angle 0.45874 ( 2) hydrogen bonds : bond 0.03947 ( 366) hydrogen bonds : angle 5.10317 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8473 (mmm160) REVERT: A 1192 TYR cc_start: 0.7491 (t80) cc_final: 0.7138 (t80) REVERT: A 1242 MET cc_start: 0.6863 (tpt) cc_final: 0.5909 (mtt) outliers start: 16 outliers final: 15 residues processed: 82 average time/residue: 0.1845 time to fit residues: 20.4837 Evaluate side-chains 84 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1093 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.132062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.104974 restraints weight = 81600.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.108730 restraints weight = 40639.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.110824 restraints weight = 26155.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.112009 restraints weight = 19749.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.112651 restraints weight = 16824.194| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7304 Z= 0.101 Angle : 0.487 6.756 9881 Z= 0.260 Chirality : 0.039 0.141 1088 Planarity : 0.004 0.041 1290 Dihedral : 4.464 59.571 954 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.02 % Allowed : 12.75 % Favored : 85.23 % 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: 0.72 (0.30), residues: 865 helix: 1.36 (0.24), residues: 469 sheet: -1.18 (0.64), residues: 67 loop : -0.35 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1067 TYR 0.011 0.001 TYR A 891 PHE 0.014 0.001 PHE A 641 TRP 0.008 0.001 TRP A 415 HIS 0.003 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7303) covalent geometry : angle 0.48692 ( 9879) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.37498 ( 2) hydrogen bonds : bond 0.03778 ( 366) hydrogen bonds : angle 4.88589 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8464 (mmm160) REVERT: A 1192 TYR cc_start: 0.7452 (t80) cc_final: 0.7095 (t80) REVERT: A 1242 MET cc_start: 0.6872 (tpt) cc_final: 0.5904 (mtt) outliers start: 16 outliers final: 15 residues processed: 80 average time/residue: 0.1772 time to fit residues: 19.4187 Evaluate side-chains 83 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 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 = 0.4512 r_free = 0.4512 target = 0.131769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.104588 restraints weight = 82111.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.108336 restraints weight = 40625.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.110307 restraints weight = 26077.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.111618 restraints weight = 19854.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.112271 restraints weight = 16890.232| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7304 Z= 0.113 Angle : 0.492 6.736 9881 Z= 0.265 Chirality : 0.039 0.136 1088 Planarity : 0.004 0.042 1290 Dihedral : 4.456 59.801 954 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.89 % Allowed : 12.88 % Favored : 85.23 % 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: 0.75 (0.30), residues: 865 helix: 1.37 (0.24), residues: 469 sheet: -1.07 (0.66), residues: 67 loop : -0.34 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.012 0.001 TYR A 891 PHE 0.011 0.001 PHE A 641 TRP 0.008 0.001 TRP A 415 HIS 0.002 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7303) covalent geometry : angle 0.49183 ( 9879) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.37968 ( 2) hydrogen bonds : bond 0.03760 ( 366) hydrogen bonds : angle 4.87339 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8458 (mmm160) REVERT: A 1192 TYR cc_start: 0.7456 (t80) cc_final: 0.7086 (t80) REVERT: A 1242 MET cc_start: 0.6825 (tpt) cc_final: 0.5907 (mtt) outliers start: 15 outliers final: 14 residues processed: 76 average time/residue: 0.1770 time to fit residues: 18.6647 Evaluate side-chains 81 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.132279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105601 restraints weight = 81208.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.109451 restraints weight = 40195.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.111613 restraints weight = 25394.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.112653 restraints weight = 19057.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.113389 restraints weight = 16357.612| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7304 Z= 0.096 Angle : 0.483 6.728 9881 Z= 0.256 Chirality : 0.039 0.141 1088 Planarity : 0.004 0.041 1290 Dihedral : 4.389 59.731 954 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.64 % Allowed : 13.26 % Favored : 85.10 % 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: 0.95 (0.30), residues: 865 helix: 1.54 (0.24), residues: 469 sheet: -1.01 (0.67), residues: 67 loop : -0.25 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.012 0.001 TYR A 891 PHE 0.011 0.001 PHE A 702 TRP 0.007 0.001 TRP A 415 HIS 0.005 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 7303) covalent geometry : angle 0.48351 ( 9879) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.37694 ( 2) hydrogen bonds : bond 0.03639 ( 366) hydrogen bonds : angle 4.72108 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.03 seconds wall clock time: 43 minutes 20.77 seconds (2600.77 seconds total)